In the context of promoting “craftsmanship”, how to improve students’ craftsmanship through scientific teaching management strategies has become an important issue in education. In this paper, a multi-objective optimization model of teaching management is constructed with the objectives of minimizing the management cost, maximizing the index of improving craftsmanship and maximizing the satisfaction of teaching. In order to solve the model, the classical NSGA-II algorithm is improved by introducing the matrix-encoded multi-crossover operator, the sub-elitist initialization population strategy, and the improved Pareto dominance relation, which enhances the convergence performance of the algorithm and the uniformity of the distribution of the solution set. Simulation experiments are conducted through the standard test function DTLZ series, and the improved NSGA-II algorithm outperforms the comparative models in DTLZ2, DTLZ4, and DTLZ7 test problems, indicating that it has a better multi-objective solving capability. An empirical study on the effect of craftsmanship enhancement was conducted based on 150 student samples, and the implementation of teaching management strategies based on multi-objective optimization can significantly enhance students’ comprehensive craftsmanship (Sig=0.001). This study provides a multi-objective optimization method for educational management department’s teaching management strategy development for reference, which has important value and practical significance.