As the center of water resource regulation, storage and dispatching in Taihu Basin, the inflow and outflow of Lake Taihu has changed with the implementation of engineering and non-engineering measures. Based on observed inflow and outflow data from 1986 to 2017, the flow variations and possible reasons were studied using Mann-Kendall trend test, mutation test and moving-t test. The results showed that annual total inflow increased significantly with the mutation point in the late 1990s, while annual total outflow increased significantly with mutation point in the late 2000s. Compared with annual flow before mutation point, multi-year inflow increased 2.966 billion cubic meters and outflow increased 1.863 billion m³. The inflow increase rate and contribution rate in Jiangsu Province were 53% and 84%, while the outflow increase rate and contribution rate were 31% and 48%, respectively. The outflow increase rate and contribution rate in Zhejiang Province were 26% and 31%, respectively, while the inflow increases rate and contribution rate did not change significantly. Among all the regions, Wangyu River has the highest inflow increase rate, with a small contribution; the outflow increase rate and contribution rate of Taipu River did not change significantly. Variations of inflow and outflow raised the annual average water level and the annual lowest water level in Lake Taihu, however, with little impact on the annual maximum water level. Increasingly importance of hydrological engineering has been attached to changing inflow and outflow of Lake Taihu.