In order to analyze the efficiency of comprehensive river regulation works on water system connectivity of small water bodies in the polder areas of Taihu Basin, two more criterion layers of landscape connectivity and water quality improvement were put forward based on the existing criterion layers including water system pattern, structural connectivity and hydraulic connectivity, due to the prominent functions of small water bodies in ecosystem protection and water purification. The conventional indices were modified according to the shape characteristics of small water bodies, so as to better describe polymorphic river networks. In light of different water flow pathways and hydraulic conditions of small water bodies caused by various regulations of hydraulic structures, structural connectivity and hydraulic connectivity were calculated separately under diverse working conditions, and then weighted by duration for relatively stable annual averages. Then, this evaluation system of water system connectivity of small water bodies was applied to the connectivity evaluation of the Tongzi River in Liyang City before and after river regulations. The results showed that comprehensive river regulation works had a significant effect on the improvement of the water system connectivity, and the evaluation system could reflect water system connectivity of small water bodies under collaborative operations of various hydraulic structures in a reasonably objective and comprehensive way.