Shiyang River Watershed is an important ecological barrier and agricultural production area in Northwest China, and the study of soil heavy metal content, distribution, and sources is important for agricultural product safety, pollution control, and ecosystem health. In this paper, 140 soil samples were collected from 28 stations to assess the level of heavy metal (Arsenic (As), Copper (Cu), Lead (Pb), Cadmium (Cd), Chromium (Cr), Mercury (Hg), Nickel (Ni), Zinc (Zn)) contamination, pollutant sources and influencing factors of soil in Shiyang River Watershed through determination of the metal contents and statistical analysis. The results indicated that the soils in the study area are typical saline soils in arid zones. The enrichment factors (EF) of As, Cr, Cu, Ni, Zn, and Pb indicate no contamination, and the EFs of Cd and Hg suggested minor contamination. Although the concentrations of Cd and Hg in soil are lower than others, they are more biotoxic and exhibit a moderate–high ecological risk. The index of geoaccumulation (I_geo) values reflect that most of the stations, especially the three groups of samples from depths of 10–20 cm, 20–40 cm, and 40–80 cm, are below the contamination threshold for all heavy metals. The chemical speciation of heavy metals, principal component analysis, and correlation analysis showed that Cr, Cu, Pb, Cd, Ni, and Zn mainly come from the natural accumulation upon weathering of soil-forming matrices. Hg and As mainly come from anthropogenic contributions. The effect of agricultural crop cultivation on soil heavy metal contamination is mainly through farm irrigation and crop–soil interactions, which accelerate the release of heavy metals through the weathering of soil-forming parent material and irrigation, which transports the heavy metals below the surface. The results of this study can provide a scientific basis for the involved authorities to formulate reasonable policies on environmental protection and pollution control.