Should I omit my master's supervisor from Referees list in PhD Application? I've finished my masters thesis and waiting for results. Meanwhile, I've started searching for PhD position. and I find out one of the requirement of one to three referee contacts, one of them preferably the masters supervisor. 

I've 3.93/4.00 CGPA with coursework and My current masters supervisor is quite satisfied with my research performance so far. He wants me to continue my PhD with him and has offered me the position as well. Whereas, I don't want to continue with him and that's why I haven't told him about my PhD plans. 

I'm confused and I'm not sure if I tell him that I don't want to my PhD with him, Will he write good remarks about me or he'll write bad remarks so that I don't get PhD position somewhere else. 

Another problem is that if I tell him straight forward that I am not interested to continue my PhD with him I might lose this opportunity as well. 

I've no one to discuss with about this issue and about my further PhD plans. Time is running and I'm becoming more and more stressful.
Should I omit my master's supervisor from Referees list in PhD Application?


Almost certainly no. Your master's supervisor is likely the only person who can actually speak to your ability as a researcher. As someone who has done well on their coursework, their recommendation is the most valuable to you. The fact that he wants you to continue with him is good! If he didn't, he probably wouldn't recommend you to anyone else!


  I'm confused and I'm not sure if I tell him that I don't want to my PhD with him, Will he write good remarks about me or he'll write bad remarks so that I don't get PhD position somewhere else.


This would be incredibly unprofessional and unethical. That's not to say that it's impossible, but you should have a good idea of whether it is likely based on your interactions with him. You should not assume this will happen unless you have a bad feeling about him already.


  Another problem is that if I tell him straight forward that I am not interested to continue my PhD with him I might lose this opportunity as well.


This is just something you will have to bite the bullet and do. Since you haven't already promised that you will do your PhD with him, he has no legitimate objection. If he is acting in good faith, he should not withdraw his offer from you. There is absolutely nothing wrong with applying to multiple supervisors. If he seems angry that you are, then you definitely do not want to do your PhD with him. Of course, he may then decide to hire someone else, so it is possible you will lose the opportunity, but this is unavoidable. You cannot have it both ways.