Fish is consumed as a common food by humans due to its nutritional and therapeutic benefits. However, they can accumulate toxic chemicals (such as heavy metals, persistent organic pollutants) from water and food chain. Very few studies have been investigated on heavy metal contents in fish from Tibetan Autonomous Region of China. In order to study heavy metals levels in fish from aquaculture farms and evaluate the risk that human consume fish in this area, we collected four types of aquaculture fish species (6 big-head carps, 5 grass carps, 5 carps and 5 tilapias) from fisheries around Lhasa city in this study. 9 heavy metals (Cr, As, Cd, Pb, Cu, Ba, Co, Mn and V) in different tissues of fish were determined by an inductively coupled plasma mass spectrometer. Cr, Ba, Co, Mn and V could easily accumulate in the gill, and Cu was detected in the hearts of all the fishes. Toxic metal (As, Cd and Pb) contents were higher in the liver than those in other tissues, heavy metal levels were the lowest in the muscle among all tissues. Most of heavy metal concentrations in the tilapia tissues were higher than those in other fish tissues, especially arsenic. Arsenic content in the tilapia samples was ~2–4 times higher than the maximum levels (MLs) of contaminants in the national standard, and other metals were all lower than the MLs. Compared the estimated daily intake of heavy metals through fish consumption with tolerable daily intakes recommended by FAO, the metals daily intake of As, Cd and Pb from fish consumption might not pose serious health risk to the local inhabitants. It is therefore necessary to determine the dose level for human, which is considered to be taken daily over a lifetime without adverse effects.