Through the online payment industry environment, industry chain and the analysis of major enterprises, built with third-party online payment core competence evaluation index system including with 14 evaluation index. BP neural network model is designed to select a sample of six training companies, three companies to test, and the use of BP neural network model quantitatively identify third-party online payment the strength of the core competence of enterprises. Studies have shown that: compared with the traditional linear model, BP evaluation mode is more dynamic and self-learning nature, the error evaluation of the results of small, high precision, fully reflects real situation of the third-party online payment enterprise's core competence, for third-party online payment to build the core competetiveness of enterprises to provide a benchmark, while the third-party online payment company for quantitative evaluation of core competencies has opened up a new way.