Runoff generation is a complex meteorological-hydrological process influenced by many factors. We analyzed the effects of changes in precipitation and soil water storage (SWS) on runoff generation using the path-analysis method (PAM) in Xinjiang River Basin (XJRB). By using multiple trend analysis we found that precipitation, SWS and runoff in XJRB fluctuated throughout the past 30 years with no monotonic trends at both annual and seasonal scales. Further analysis demonstrated that runoff is more sensitive to precipitation than to SWS in XJRB. PAM results showed that direct influence of precipitation on runoff was seven times as large as that of SWS. Moreover, the indirect influence of precipitation on runoff through SWS accounts for 11–31% of the total influence of precipitation on runoff. This information will improve the description of precipitation and runoff relationship as well as the planning and management of water resources.