Heavy metals have long been recognized as pollutants that are potentially harmful to human health. In recent decades, research on heavy metals in soil environments has become a hotspot in environmental research. Under normal conditions, heavy metal concentrations in soils are several orders of magnitude higher than that in the background value of soils. Thus, the concentrations and potential ecological risks of heavy metals in farmland soils are important reference indicators for evaluating farmland soil environmental quality. Human activities are known to result in heavy metal pollution of farmland soils. Recent research in this field in China has focused on the sources, distribution, pollution, and ecological risk of heavy metals in farmland soils in the eastern or central parts. However, there has been limited research on soil contamination of farmland, particularly pepper fields, in the arid regions of northwest China. Therefore, we collected a total of 105 soil samples from pepper field in the main pepper production area (Yanqi Basin) in Xinjiang, China, and determined the content of eight heavy metals (As, Cd, Cr, Cu, Mn, Ni, Pb, and Zn) by standard methods. The heavy metal pollution of pepper field soils was analyzed based on pollution load index (PLI), potential ecological risk index (RI), and ecological risk warning index (I_ER). The results indicated that the average content of Cd, Cr, Ni, Pb, and Zn exceeded 1.65, 1.40, 1.32, 3.21, and 6.42 times, respectively, that of the background values for irrigation soil in Xinjiang. High levels of Pb, and Zn pollution, low levels of Cd, Cr and Ni pollution, and no As, Mn, or Cu pollution were detected in pepper field soils. The average value of PLI was 1.40, which showed a light pollution level; the average RI for each heavy metal in decreasing order was as follows:Cd, Ni, As, Cu, Pb, Cr, and Zn. The average value of RI of soil was 18.40, which indicated light ecological risk. The average value of I_ER of soil was -4.78, which indicated a no warning situation. The pollution level, potential ecological risk, and ecological risk warming of Bahrash county were the highest, whereas those of Hejing county were the lowest in Yanqi Basin. As, Cd, Pb, and Zn pollution in pepper field soil were mainly affected by the human activities, and Cr, Cu, Mn, and Ni pollution were mainly affected by the geochemical background of soils. Cd was the main pollutant of farmland soil with strong influence on the PLI, RI, and I_ER. The pollution risk of Cd should be a major concern during the process of agricultural production in Yanqi Basin.