This paper investigates the positive influencing factors and the degree of influence of authentic university–enterprise cooperation on the employability of cross-border e-commerce graduates. We used the literature analysis method and Delphi method to construct 12 factors affecting employability and put forward corresponding hypotheses. We tested the data and correlation analysis by SPSS software and used structural equation modeling for parameter estimation and path coefficient measurement to construct a relationship model of the factors influencing the employability of college students by cross-border e-commerce university–enterprise cooperation. The results show that the university–enterprise authentic cooperation has positive impacts on college students’ employability in theoretical knowledge, learning, professional skills application, personal basic quality, and professional quality. With the rapid development of cross-border e-commerce, studying the factors that affect the employability of college students through university–enterprise cooperation can not only promote the further integration of industry and education but also further improve the employability of college students, thus promoting the development of social economy. Therefore, the research is of positive significance.