This paper discusses the implementation and application of MATLAB tools in the teaching of engineering majors so as to improve the quality of education and students’ mathematical application ability. Using the programming and GUI graphical interface design functions of MATLAB, the method of establishing the graphical user interface of the mathematical experiment module closely links the experimental content with the practical teaching of mathematical modeling. With the help of the operation functions provided by the system, we can set the experiment parameters and design the experiment interface ourselves to deepen our intuitive understanding of the mathematical content learned. After the pilot teaching in the mechanism major of University Z, 22 individuals failed to reach course objective 1, and 40 individuals were unable to reach course objective 2. The number of individuals passing the three lab reports increased continuously, from 40 to 57 in Class 1 and from 34 to 56 in Class 2. The math scores in the three exams improved significantly, and the distribution of the scores went from concentrating on scores below 60 to focusing on scores between 70–89. As a result, the teaching method for MATLAB tools application was effective.