Selenium (Se), zinc (Zn), calcium (Ca), iron (Fe) and other elements have positive effects on human health, and the contents of these functional mineral nutrients in soil affects their contents in crops to a certain extent. In order to understand the distribution and possible influencing factors of functional nutrient elements in farmland soils and crops in Southeast Xizang, this study analyzed the contents of total Se, Zn, Ca and Fe in farmland soils and crops in 5 counties (districts) of Nyingchi City of Xizang. The results showed that the contents of total Se, Zn, Ca and Fe in farmland soils were 0–0.48 mg/kg, 37.96–194.17 mg/kg, 2.41–7.30 g/kg and 10.20–34.35 g/kg, respectively. Among the tested soil samples, 64% did not reach the appropriate level of Se, 85% did not reach the medium level of Fe, 76% reached the medium and abundant levels of Zn. The contents of Se, Zn, Ca and Fe in farmland soils decreased with the increase of altitude. There was no significant correlation in Se, Zn and Ca contents between grain and soil except Fe which had significant positive correlation (P<0.05). The above results showed that the farmland soil in Southeast Xizang is deficient in Se and Fe, but there are more Zn-rich soils. The zinc–rich farmlands in some areas can be further tracked and studied to make full use of regional soil resources to develop local characteristic agricultural and sideline products.