Grace has given a good answer. You can also use this phrase to tell someone to take a more positive view of something that could be either good or bad. For example: A: "Why do my coworkers always ask me so many questions?" B: "Maybe it's because they think you're smart. Just take it as a compliment." In this scenario, A seems to be irritated about having to answer so many questions. B tries to make the situation better by suggesting that A should "take it as a compliment," instead of being irritated about it.

Hey Ramin! The sentence “Just take it as a compliment” means that you should not be offended by whatever the person might have said to you. For example, if someone were to tell me that I look like an English professor, I should accept the statement as a compliment rather than an insult (though arguably, it could be interpreted as either one). Does that make sense to you? If not, I will attempt to clarify! ~Grace