To "think it over" means to think about something that you have to make a decision on. In the example above, the job applicant has to "think over" whether to take the job.
This expression almost always uses "it":
Let me think it over.
If you don't use "it", the word order changes:
Have you thought over my offer?
A more formal word that means something similar to "think it over" is "consider". You would write this if you were offering someone a job in writing:
Please consider our offer and let us know what your decision is by next Thursday, March 10th.