In order to accurately and objectively evaluate the level of regional water resources carrying capacity (WRCC), from the perspective of WRCC evaluation samples and evaluation level standards, set pair analysis semipartial connection number (SCN) and subtraction set pair potential (SSP) method were applied in this study. A mobility matrix which quantitatively reflects and describes the micro movement between the connection number components (CNCs) in the connection number system structure was constructed, along with a correction method on CNC values. Meanwhile, the difference coefficient was dynamically determined based on SSP and triangular fuzzy number method, and the quantitative evaluation method of regional WRCC was constructed. The application of this method in Huaibei City, Anhui Province showed that WRCC in 2011-2019 was between level 2-3, and the carrying capacity was relatively poor. The overall system situation transited from partial inverse potential to equilibrium potential, and gradually developed for the better. In judging the development of system situation, the connection number value based on SSP changed from -0.279 in 2011 to -0.037 in 2018 and then to -0.218 in 2019, and connection number value based on SSP changed from -0.267 in 2011 to -0.035 in 2018 and then to -0.207 in 2019. Results indicated that both methods were applicable, with the latter one better in determining the evaluation grade value and relative error < 1 %, which was related to the more profound physical interpretation of the semipartial SSP. The micro motion results between the CNCs in the structure of the connection number system showed that the value of the largest component in the original connection coefficient will decrease, and the changes of the other two components are related to the size of the component itself, the proportion of the increment represented by the SCN to the original CNCs, and the size of the migrated original CNCs. Based on the SCN and dynamic SSP method, the correction and updating of connection number and the dynamic determination of difference coefficient can be realized. The method has strong physical interpretation and accurate and reliable evaluation results, which provides a new and effective way to accurately distinguish the state and overall development trend of complex water resources system from the perspective of system structure and genetic mechanism.