The main purpose of this paper is to study the weighting analysis of influence factor in water quality by using grey system theory. First of all, we present the GM(h,N) model in grey system theory for our need. Second, an example of Chaohu Lake in China is provided, and the main influence factors of water quality are analyzed, which include eight factors: pH, dissolver oxygen (DO), permanganate, non-ironic ammonia, total phosphorous (TP), total nitrogen (TN), transparency and chlorophyll. Then, using GM(h,N) method in grey system theory, we derived the factors' weighting and relational of water quality. Besides, in this paper, we also apply Matlab to support the calculation and verification our approach. As a result, it is in good agreement with the actual situation; finally, some further suggestions are indicated for the research in the future.