Due to the lack of available long-term climatic records, data related to past autumn precipitation variability throughout Northwest China, especially high-frequency variation, remains limited. In this study, it was found that inter-annual changes in Qinghai spruce radial growth were significantly and negatively (p < 0.05) correlated to inter-annual differences in precipitation during the late growing season (September-October) at all sampling sites in the upper reaches of the Heihe River. Based on the growth-climate relationship, a reconstruction of the inter-annual variation in September-October precipitation from 1839 was developed. With the help of this reconstruction, we successfully captured increased inter-annual variations in September-October precipitation during 1855-1861, 1892-1902, and 1969-1986. Furthermore, we found that increased precipitation variation might be related to variation in the westerlies and instability in the relationship between the regional westerly and precipitation. Moreover, our reconstructed data significantly correlated to the drought index (i.e., October SPEI_01) and moisture-related parameters (i.e., September-October cloud fraction), suggesting that our reconstructed data could be used as an indicator of the drought condition in the Heihe River Basin during the late growing season.