The change trend of future runoff in the middle and upper reaches of Jinsha River Basin was investigated to provide some technical support for the planning of flood control in the basin. Based on the SWAT hydrological model, the CMIP5 data set was selected to establish a global climate model for the future period of 2022-2050, and the runoff change trend in the study area was analyzed from the temporal and spatial scales. The results show that the precipitation and temperature in the basin from 2022 to 2050 are both higher than those in the base period, and show an upward trend, with a large increment in rainfall in the south of the basin and a large increment in temperature in the north of the basin. Under the three scenarios of RCP2.6, RCP4.5 and RCP8.5, the runoff from 2022 to 2050 all show an upward trend, and the change rates are 579×106 , 553×106 and 299×106 m3/a, respectively. Compared with the base period, the future spring and autumn runoff show an downward trend, whereas the summer and winter runoff show an upward trend, with the largest increment in winter, reaching 10%. The runoff yield increases sequentially from northwest to southeast; compared with the base period, the runoff yield in the south of the basin presents an increasing trend. The results indicate that the runoff will show an increasing trend in the future, with a greater increment in winter, and extreme hydrological events such as winter floods may occur; in the future, the threat of floods in the southern basin may further aggravate.