Im confused when it comes in two accusatives in indirect statements.
How do I say "I think she loves me" without sense of "I think I love her"?
I get the translation as - Cogito/arbitror ei me amare.
You have encountered a well-known problem with the Accusativus cum infinitivo (AcI) construction.
There is a famous story. You have perhaps heard of king Pyrrhus, a Greek king from the Aeacid dynasty who once won a battle (at Asculum) and lost so many men in the process that he reportedly said: “One more victory like this, and we are doomed” – giving rise to the expression Pyrrhic victory. That was actually a battle against the Romans, because Pyrrhus had put it in his head to invade Italy and “liberate” the Greek colonies there. He eventually failed, having to retreat from Italy after the Battle of Beneventum.
But before Pyrrhus made this ill-fated foray into Italy, the story goes, he had visited the famous Oracle of Delphi and sought advice on his chances in a war against the up-and-coming Romans. The Pythia replied:
Aio te, Aeacida, Romanos vincere posse.
… and so Pyrrhus went to war confident that the Oracle had said he “could defeat the Romans.” But the Oracle was not wrong, was it? It had, after all, predicted that “the Romans could defeat him.”
(By the way, Cicero was not convinced by this story, which he attributed to Ennius. For one thing, the Oracle of Delphi did not speak Latin. And in any event, even if it had, Pyrrhus should have noticed the ambiguity.)
To answer your question, though, there is not much you can do within the confines of the AcI that would disambiguate the sentence. (Actually that is not quite correct. As answered by Joonas, you can use a passive infinitive.) The correct Latin is:
Puto eam me amare.
… and it is simply ambiguous.
One possible solution in addition to those outlined in Joonas' answer is to use the “factual quod,” but it is an unusual construction. In fact, the dramatist Plautus once found himself in a similar position as you do. He wanted to write: “I already know that my son loves that prostitute (meretrix).” But if he had written: Scio filium meum istanc meretricem amare, it could very well also have meant: “I already know that that prostitute loves my son.” Here's what he wrote (Asinaria, act 1, scene 1):
Equidem scio iam, filius quod amet meus istanc meretricem.
Note Plautus puts the subordinate clause in the subjunctive, but you do not have to do that. In Medieval Latin, this became a commonplace way to express indirect speech, and there is another question about whether to use the subjunctive or indicative.
So here is what you can write:
Puto, quod ea me amat (or amet).
My personal feeling is that it sounds more natural with a demonstrative pronoun:
Id puto, quod ea me amat.
That I do believe, that she loves me.
The standard choice is accusativus cum infinitivo where both the subject and object are in the accusative and the message is inherently ambiguous. You can read puto me eam amare as "I think I love her" or "I think she loves me".
I would suggest a couple of ways around this ambiguity in general:
Use an agent with a passive: Puto me ab ea amari is "I think I am loved by her" without ambiguity.
Use accusativus cum participio instead: Puto eam me amantem is "I think she loves me".
In this particular case the ambiguity is still there. This only makes a difference if one of the two is neuter and the other one is not. You can disambiguate between "I think I will eat the animal" and "I think the animal will eat me".
It should be noted, though, that this second option is mainly used for verbs of observation like videre. But the extra licence taken to use it with putare doesn't sound outrageous to me; it gives a perfectly understandable and concise wording without passivization.
Use a construction that does not use an accusative object: For example, puto me ei carum esse is "I think I am dear to her". Look for ways to reformulate love in a way that uses a dative so that ACI does not lead to two accusatives.
Joonas's passive version, puto me ab ea amari, is the most obvious (I don't mean that disparagingly) and straightforward way to avoid the potentially ambiguous double accusative in indirect statement; still, here are some of the numerous other ways of unambiguously expressing the same basic idea:
puto eam amore mei incensam/affectam/captam (esse).
'I think she has been kindled/affected/seized with love of me.'
puto amorem mei eam invasisse/subisse.
'I think love of me has come over her.'
(Dative ei would be somewhat more typical with subisse than accusative eam, but accusative is also found and, importantly, shows the gender in this instance.)
puto eam mei amantem (esse).
'I think she is loving of me.'
puto mihi contigisse ut ab ea amarer / puto mihi contigisse ab ea amari.
'I think it has fallen to my lot to be loved by her.'
puto accidisse ut ab ea amarer.
'I think it has come about that I am loved by her.'
In short, as this list and the other answers show, a writer who is concerned about the readers' ability to use context (including, perhaps, word order) to resolve the pronouns in these types of sentences has many options for avoiding the ambiguity.
Other possibilities: