In response to the common teaching problems in undergraduate mathematical modeling courses, such as tight teaching time, complex knowledge system, disconnection between theory and practical competition, single teaching method, and one-sided evaluation system, this paper will adopt the educational concept of outcome-oriented learning, and support it with the theory of constructively aligned and cognitive load theory. It will construct a new teaching model different from traditional numerical courses. With the goal of cultivating students’ knowledge, ability, and quality in three dimensions, the course modules will be reorganized. Through online self-study to carry out low-level cognitive tasks and offline classes to focus on high-level modeling thinking discussions, a three-level project training system of basic practical operation, comprehensive application, and innovative expansion will be designed. Finally, an assessment mechanism combining comprehensive process evaluation and final evaluation will be established. Teaching practice has shown that this collaborative teaching model can effectively resolve the contradiction between teaching time and teaching content, help students build modeling thinking, and improve their abilities of question analysis, model design, algorithm implementation, and team scientific and technological innovation. This teaching model can provide a reference for the teaching reform of similar applied mathematics courses in universities.