This paper investigates and analyzes the optimal allocation of educational resources and the expansion and innovation of the content system of e-commerce English courses in vocational education institutions in Fujian and Taiwan, and proposes methods and strategies for the optimal allocation of educational resources and the innovation of the course system. The evaluation index system of educational resources allocation was established, the factor analysis method was used to establish the educational resources allocation measurement model of vocational colleges and universities, and the K-Means clustering algorithm introducing profile coefficients was applied to cluster vocational colleges and universities on the level of educational resources allocation. The study classified 42 vocational colleges in Fujian and Taiwan into four categories, and based on the results of cluster analysis and factor ranking, the four categories of vocational colleges put forward suggestions for optimizing the allocation of their own educational resources allocation level. The results of the curriculum system innovation practice show that after the teaching design of the e-commerce English curriculum system innovation, the performance of the experimental class is significantly higher than that of the control class, increasing from 22.84 to 26.81 points. It shows that the teaching design of ecommerce English course system innovation is suitable for the needs of English teaching and can provide important guidance for teachers of e-commerce English in vocational colleges and universities when they are teaching.