Nagqu is affected by monsoon climate, plate geology movements, and complex terrain and other disaster-causing factors, it is a natural disaster-prone, contiguous and frequent region. The annual average temperature is , while the coldest temperatures can reach minus . Overall it classifies as a dry-winter subarctic climate (Dwc) bordering on a cold semi-arid climate (BSk), with relatively warm, humid summers and long, bitterly cold, dry, windy winters. The differences between day and night are severe. It is not uncommon to have nights with temperatures below freezing after days with temperatures of or days with temperatures above freezing in winter after night temperatures of . The annual sunshine hours are more than 2,886 hours. Nagqu city had an average annual rainfall of between 1956 and 2010. The southeastern part of the prefecture is wetter, with annual precipitation exceeding . while the northwestern part is dryest with an average annual rainfall below . The effects of global warming increasingly pose a problem in the region, with record highs in 2019.
