[Objective] The objective of this study was to analyze the characteristics and causes of the spatial-temporal changes of the annual runoff and annual sediment at the main hydrologic stations on the stem stream of the Heihe River, in order to provide decision basis for the ecological environment protection and water resource utilization.[Methods] The runoff, sediment and rainfall data form main hydrologic stations on the stem stream of the Heihe River during 1956 to 2015 were collected. Methods including Mann-Kendall trend test, cumulative anomalies and correlation analysis were applied.[Results] The results indicated that the runoff of the upper reaches of Heihe River had an obvious increasing trend from 1956 to 2015, with high flow during the period from the 1980s to the 2000s. Meanwhile, the sediment load was in a slightly increasing trend from 1970s to 2000s, but the sediment load of the Yingluoxia station had an obvious decreasing trend from 2001.[Conclusion] The increasing precipitation was one of the main contributions to runoff rise. In addition, the soil erosion caused the increase of the annual sediment load of the Zhamashike and Qilian station. Sediment captured by water reservoir was found to be the major cause of the decrease of sediment load in the Yingluoxia station.