The Naoli River Basin is the largest basin on Sanjiang Plain. Its runoff variation plays a crucial role in the development of social economy and ecological environment change of Sanjiang Plain. In order to obtain the variation characteristics of runoff series, the linear trend analysis and Mann-Kendall test were used to analyze the trend of runoff series of four representative hydrological stations in Naoli River Basin. Then the moving cut data-approximate entropy (MC-ApEn method) and Mann-Kendall mutation testing were used to check the mutation characteristics of runoff series. Also the mutation reason of the runoff series was discussed. The results showed that the runoff volume of Naoli River was distributed unevenly and the annual runoff of the same hydrological station had great variation. It was not conducive to the full use of water resources in Naoli River Basin. Runoff series showed obvious reducing trend in the recent 50 years, and the runoff of the Baoqing Station, the Baoan Station and the Caizuizi Station decreased obviously. The runoff mutations of Naoli River occurred in 1966, after the abrupt change, there is an obviously decreasing trend of runoff which is large because of reduced precipitation, increased urban residents water consumption and the growing number of construction of water conservancy. The moving cut data-approximate entropy in the process of runoff mutation analysis showed the characteristics of high precision, strong antiinterference ability and so on and it is a method for detecting the mutations of nonlinear time series.