It is challenging to evaluate non-point source pollution (NPSP) quantitatively and comprehensively in a basin without gauged data. In this paper, the export coefficient model (ECM), source strength coefficient method (SSCM), and the equivalent pollution loading method (EPLM) were integrated to evaluate NPSP in the Xiao’ anxi River Basin (XRB) in 2018. The results showed that NPSP is the primary pollution type in the study area for 68.1% of the total pollution load. The primary pollutant was total nitrogen (TN), which accounted for 56.16% of total pollution. Moreover, rural residents living sewage accounted for 48.81% of NPSP was the primary pollution source. The evaluation results are consistent with field investigation, which indicates that the proposed integration method is capable of NPSP assessment in the ungauged basin. In addition, the hydrological analogy method and the Q-V linear fitting were used to determine the discharge and flow velocity to calculate water environment capacity, and compared with the prediction of NPSP in the study area in 2022. It was found that the critical rehabilitation regions are Bachuan Town, Nancheng Town, and Er'ping Town. Furthermore, the primary pollutants, TN and total phosphorus (TP) exceeded the water environmental capacity by 76.67% and 48.58%, respectively.