Knowledge of temporal and spatial distribution of erosion is the key to understanding the climate-tectonic interaction and topographical evolution of mountain belts and to making clear the long debate whether erosion is controlled by tectonics or climate. The newly developed cosmogenic nuclides method provides us with an advanced and convenient tool to measure millennium basin-wide erosion rate, allowing us to analyze its relationship with modern climatic, geomorphic and tectonic factors. Hence, we adopted the ¹⁰Be method to investigate the basin-wide millennium erosion rates of Northern Qilian Mountains and aimed to find the controlling factors of erosion rates of this area. We collected and analyzed 9 samples from Heihe River and the front of the Northern Qilian Mountains. Our results, together with published ¹⁰Be derived erosion rates in this area, showed that the erosion rates of the basins we studied ranged from 18.7 mm/ka to 833 mm/ka, and that the weighted average erosion rates of the middle section of the Northern Qilian Mountains was about 323 mm/ka. Spatial distribution of erosion rates and correlation analysis reveal that the basin-wide erosion rate was nonlinearly correlated to the basin average slope, while no apparent correlation between erosion rate and precipitation was found. Altogether, it indicated that the slope or terrain steepness was the major controlling factor on erosion rate of the Northern Qilian Mountains area. By comparing the basin-wide average erosion rates and the vertical slip rates of faults of the Northern Qilian Mountains, our research also revealed that the surface erosion rates generally agreed with vertical slip rates of the Northern Qilian Mountains faults, implying that the Northern Qilian Mountains area was experiencing topographical uplift and outgrowth.