Abstract: Heavy metals are important factors affecting water safety, because they have strong biological toxicity and biological chain enrichment effect, and can enter water through mining, chemical industry, pesticide fertilizer, atmospheric deposition and soil erosion. The Niyang River is located in the southeast of Tibet Autonomous Region and on the left bank of the middle and lower reaches of the Yarlung Zangbo River, it is the second largest tributary of the Yarlung Zangbo River. The basin spans the subtropical, plateau temperate, plateau subtropical and plateau frigid climatic zones, and basically contains the typical characteristics of the rivers in Tibet. The Niyang River Basin is mainly distributed in the whole area of Gongbu Jiangda County and some towns in Bayi district, and its upper and middle reaches is rich in mineral resources. The study set up 10 stations along the Niyang River trunk stream at altitude of 2 910-4 677 m. Water samples were detected in wet season, normal season and dry season and the sampling period was from 2016 to 2017. The spatial-temporal characteristics, correlation and migration mechanisms of Zn, Cu, Mn, Cd and Fe in the Niyang River were studied, and the heavy metal pollution risk were evaluated. The results showed that the content of heavy metals at the source of Niyang River was low, and there was a sudden change in the middle and upper reaches, because the area was close to the rich mining area. Zn and Cu content in the whole river reach did not exceed Class II water quality standards in the whole year. Fe and Mn exceeded the standard of drinking water at the altitude of 3 500-4 500 m. Cd content changed most dramatically in time and space. Fe, Mn and Cd were sensitive factors affecting the water quality. The contents of Zn, Cu and Mn in Niyang River during the normal season were higher than those during the dry and wet season. Cd content of Bayi urban reach was the maximum in the whole year, and that during the normal season were higher than those during the wet and dry-season at an altitude of over 3 500 m. Fe content was lowest in wet season, that above 4 000 m in dry season were higher than that in normal season; At lower than 4 000 m, that of the normal season were higher than that in dry season. The contents of Zn, Cu, Mn and Fe in the normal and dry season were mainly affected by natural processes. Cd content in dry season was mainly affected by human activities. The heavy metals content in wet season should be mainly affected by human activities and hydrological and meteorological activities. The reservoir had a certain effect on the content of heavy metals. Heavy metal pollution was relatively light in river source and middle or lower reaches, but the comprehensive heavy metal pollution index in upper and Bayi City reaches was maximum. As the Niyang River is the second largest tributary of the Yarlung Zangbo River, and it has general climate, underlying surface and hydrological characteristics of the Tibetan River, so the research results had some general significance.