That's a good question. I guess that like most native speakers, I just know which to use, and don't think about it much. There are two good answers at http://english.stackexchange.com/questions/54417/proficient-in-at-with-what-is-the-correct-usage My preferred answer says: "proficient in" is generally used when discussing a subject area: "proficient in science", "proficient in auto mechanics", etc. "proficient at" is used with a specific activity: "proficient at swimming", "proficient at building houses". However, there is a third one, which you have not mentioned: "proficient with" is used when discussing a tool of some sort: "proficient with a hammer", "proficient with the violin".

...in maths would be better.

@Joyce: Thank you. But we also have "be good at Math" can we use "be proficient at Math"?

'Proficient' means 'skilled and experienced' 'be proficient at...' has similar usage to 'be good at...' + a particular skill, such as cooking, driving stuff like that Jack is good at cooking. VS Alice is proficient at cooking. -> Alice is better than Jack in terms of cooking. "Proficient in" + an area, which can be a little bit broader, such as a language or a subject e.g., Among children of parents with a low level of education, only 17% were proficient in maths. I hope it helps and look forward to hearing others' opinions.