On the basis of evaluation index system of Chaohu Lake water quality security and its grading criterion, an objective weight structure of evaluation indexes consisted of attribute weights and sample set weights is proposed, the attribute weights can be computed using accelerating genetic algorithm based correspondence factor analysis, the sample set weights can be computed using accelerating genetic algorithm based projection pursuit method, the objective combination weights of evaluation indexes can be computed using minimum relative information entropy principle, which forms a model for evaluating Chaohu Lake water quality security, named CFA-PP for short. The applied result of CFA PP shows that the most important four indexes are total phosphorus, chlorophyll a, ammonia nitrogen and total nitrogen, respectively; the water quality security grade of the whole lake is between “relative insecurity” and “insecurity” grade; the most effective approach to improve water quality security of Chaohu lake is to reduce influent trophic salt loads of phosphorus and nitrogen. As a general evaluation method driven by data, CFA-PP can be widely applied in different water quality security evaluation.