Impact of Recommendation letters I am a master’s student of pure mathematics at my country’s most famous university, and recently I have applied to a couple of foreign universities.

Because of the reputation of my university and my high average which is around 19.50 out of 20, and also my master’s project which is going to be published in an accredited international journal, I am optimistic to be admitted for a PhD position abroad.

However, the most reputed and cited professors do not write a letter of recommendation for me because my major is not their area of expertise. My supervisor does not have many citations on google scholar. Will it affect my admission process?
I don't think that you have much to concern you. You can't get a letter from someone who won't write one, of course, but if your own advisor is on the faculty of such a university the assumption is that his/her word can be trusted. 

What you need is someone who knows you well and can speak honestly about your background and prospects for success. Your advisor is best placed to do that and support you. The superstars, if they could be convinced to write, would probably need to say things less directly applicable or useful to you. 

You need to put together a good case that you are well prepared and are likely to succeed. Your advisor's letter will help with that.