The Junggar Basin in Xinjiang is located in the hinterland of Eurasia, where the groundwater is a significant resource and has important ecological functions. The introduction of harmful organic pollutants into groundwater from increasing human activities and rapid socioeconomic development may lead to groundwater pollution at various levels. Therefore, to develop an effective regulatory framework, establishing a list of priority control organic pollutants (PCOPs) is in urgent need. In this study, a method of ranking the priority of pollutants based on their prevalence (Pv), occurrence (O) and persistent bioaccumulative toxicity (PBT) has been developed. PvOPBT in the environment was applied in the screening of PCOPs among 34 organic pollutants and the risk assessment of screened PCOPs in groundwater in the Junggar Basin. The results show that the PCOPs in groundwater were benzo[a]pyrene, 1,2-dichloroethane, trichloromethane and DDT. Among the pollutants, benzo[a]pyrene, 1,2-dichloroethane and DDT showed high potential ecological risk, whilst trichloromethane represented low potential ecological risk. With the exception of benzo[a]pyrene, which had high potential health risks, the other screened PCOPs had low potential health risks. Unlike the scatter distribution of groundwater benzo[a]pyrene, the 1,2-dichloroethane and trichloromethane in groundwater were mainly concentrated in the central part of the southern margin and the northern margin of the Junggar Basin, while the DDT in groundwater was only distributed in Jinghe County (in the southwest) and Beitun City (in the north). Industrial and agricultural activities were the main controlling factors that affected the distribution of PCOPs.