How to reuse/cite your paper in your thesis when both have same topic
Now I want to submit my thesis but I suppose it is self-plagiarism if I don't cite my paper. 


Self-plagiarism isn't relevant here, your thesis isn't considered published.




  My question is, can use the same content in my thesis 


Yes.


  then how do I mention that content is reused? 


You can mention something along the lines of: This manuscript is based upon my PhD thesis [1].


  or should I rephrase my complete thesis now 


There's no need.


  But if I rephrase then how about the experiment results and figures?


Again, there's no need.


  should I cite paper there as well?


Citing your thesis once suffices.