Nyingchi Valley is one of the most important agricultural areas on the Tibetan Plateau, and soil degradation has become more and more severe there with the development of agriculture. Fertility indexes and heavy metal concentrations of soil samples from the representative fields in Nyingchi Valley and heavy metal concentrations in corresponding wheat and vegetable samples were investigated. The results showed that soil organic matter, alkali-hydro nitrogen and total nitrogen were from moderate to low levels. The concentrations of total phosphorous, potassium and bioavailable zinc were at low level, but bioavailable phosphorous, potassium and copper were abundant. Soil organic matter played a key role in the preservation of soil fertility. The concentrations of copper, zinc and cadmium in both soil and plant were all lower than the corresponding national standards. However, the accumulation of copper, zinc and cadmium occurred in topsoil in Nyingchi Valley and could be attributed to over farming.