Based on the data of measured monthly runoff from the source flows and the main stream of Tarim river from 1957 to 2008, the article analyzed the variation tendency of runoff in the flood season and predicted the possible runoff of source flows and the main stream of Tarim river from 2009 to 2025 with Mann-Kendall nonparametric test and wavelet transformation. In the recent half century, surface runoff at source flows of Tarim River increased from July to September, and surface runoff of main stream of Tarim river decreased in the same period, which reflected that the increasing water consumption of the source flows took up the water resource in the main stream of Tarim River. The prediction shows that during the period of 2009 to 2025, the annual mean surface runoff of the source flows in Tarim River in July and August will belong to flat partial wet period,and that in Sep tember will belong to partial wet period; the surface runoff shows an increasing trend in July and September, and shows a decreasing trend in August. From 2009 to 2025, the annual mean surface runoff of the main streams in Tarim River in July belongs to flat partial wet period, and that in August and September belongs to partial wet period; the surface runoff shows an increasing trend in July and August, but that in September don't increase obviously or shows the trend of decrease.