With the increasing development of electronic computers and the popularization of computer technology, management systems have been widely used in the society. With the continuous improvement of the teaching system, the methods of education and teaching are also quietly changing, especially in the field of higher vocational education. Due to the characteristics of vocational education, it makes “training project progress control” and “teaching resource integration” the teaching requirements of “distribution,” “strictly restricting daily work habits,” “improving professional quality,” and “teachers’ effective control of the quality of students’ personal projects” that have become increasingly urgent needs in vocational colleges. There is a certain gap between the standards and quality of talent training in our country’s applied undergraduate colleges, and the society’s requirements for high-skilled talents and practical teaching in applied undergraduate colleges are a necessary condition for cultivating high-skilled talent. This subject research takes the mechanical manufacturing professional practice teaching system as the research object, conducts in-depth investigation and research in applied undergraduate colleges, explores the status quo of the mechanical manufacturing professional practice teaching system of applied undergraduate colleges, and analyzes the reasons for the problems. In this study, six classes of mechanical manufacturing majors in six applied undergraduate colleges were selected as the experimental group and the control group for comparison. The experimental group adopts an embedded mechanical manufacturing professional teaching system based on deep learning. In daily teaching, the control group used traditional teaching methods to learn. The questionnaire understands the role of the embedded machinery manufacturing professional teaching system in teaching from four aspects: practical teaching curriculum, practical teaching content, practical teaching equipment, and practical teaching teachers. Experiments have proved that more than half of the people think that the teaching effect of the current mechanical manufacturing professional practice teaching courses is average; only 17.18% think that the classroom is good, and 24.36% think that the classroom is poor. This shows that the construction of similar engineering professional practice is in line with the major itself, and the teaching system has theoretical guiding significance, which is conducive to the seamless connection of mechanical manufacturing majors and industrial positions in applied undergraduate colleges; it is conducive to continuously improving the core competitiveness of mechanical manufacturing majors in industrial and applied undergraduate colleges.