The adaptation of water resources system is considered to be an effective way of mitigating the effects of climate change. In view of the mechanism for water resources system adaptability under changing environment and the problem of the synthesis of two-dimensional factors in the analysis of water resources system, we analyzed the response of water resources system to the changing environment, and found that its adaptation is consisted of natural resilience and artificial adaptation. And then a systematic analysis method based on connection numbers-fuzzy risk matrix was proposed with the essence of risk matrix, in which the pessimistic and optimistic evaluation criteria were established with the evaluation interval of ［Apess，Aopt］. Case analysis of Huaihe River Basin in Anhui Province show that the adaptability level of Huaihe River Basin in Anhui Province is ［2.711, 3.833］, which is classified as “weak adaptation” under the pessimistic criterion and “moderate adaptation” under optimistic criterion. It is suggested that multiple measures should be taken to improve water quality and eco-environment quality, and thus to enhance the adaptation level of water resources of Huaihe River Basin in Anhui Province.