The integration of industry and education is an important model for building high-level higher vocational colleges and universities, and it is also a necessary way to promote the modernization and development of higher vocational education. Based on Hall’s three-dimensional structural model, this paper explores the specific process of the construction of industry-teaching integration of high-level, high-quality courses and evaluates the effectiveness of the construction of industry-teaching integration of high-level, high-quality courses using the network SBM-DEA model. The evaluation index system was first constructed according to the questionnaire survey method, Delphi method, and hierarchical analysis method, and then the indexes were screened and applied to the empirical analysis of the effectiveness of the construction of industry-teaching fusion of higher vocational boutique courses. The average overall operational efficiency of the industry-teaching fusion of boutique courses at 45 higher vocational colleges and universities is 0.547, which is the average level. However, the efficiency of the two phases still has some differences between the average efficiency value of the resource construction phase and the outcome output phase. The correlation coefficient between the efficiency of the outcome output stage and the overall operational efficiency is 0.885, which is highly correlated. Most institutions pay more attention to the operation of the outcome output stage. The R² of the fit between pure technical efficiency and comprehensive efficiency is 0.731, and the R² of the fit between scale efficiency and comprehensive efficiency is 0.264, indicating that pure technical efficiency is the dominant factor affecting the comprehensive efficiency of institutions. In the two stages of resource construction and output of results, the output side shows insufficient output, while the input side shows input redundancy, indicating that the input resources are not effectively utilized. This paper provides a direction of action to strengthen the deep integration of industry and education in higher vocational boutique courses and to promote complementary resources and a benign interaction between schools and enterprises.