in a way that is based on reason and clear thought, rather than emotions

You can't assume that people will always behave rationally. 你不能假设人们的行为总是合理的。

Rationally, he knows that she won't go back to him, but emotionally he can't accept it. 理智上他知道她不会再回到他身边，但在感情上他无法接受。