Entrepreneurship is one of the driving forces of economic development in the new era, but entrepreneurship is also highly risky behavior. The goal of constructing the entrepreneurial interactive decision-making model and entrepreneurial project system model is to provide a theoretical reference value for entrepreneurial teams through simulation experiments. The conceptual model of entrepreneurial team interaction decision-making is constructed based on multi-intelligence under the support of relevant theories, and the main influencing factors affecting the interaction decision-making are analyzed and the specific decision-making model is designed on the basis of this. Then, according to the ideas and principles of system dynamics, the boundary of the system is delineated, the scope of research is clarified, the structure of the system is analyzed, the levels of the system are delineated, and the feedback mechanism of the system is determined. The relationship between the system levels is analyzed, feedback loops and causality diagrams are established, and in this way, a mathematical and canonical system dynamics model is established, and finally, simulation prediction and hypothesis testing are carried out. The regression results show that there is a positive effect of mutual influence among the three variables of the interaction decision model: team initiative, team decision performance. The error between the values of this paper’s model for simulation and the actual values is less than 10%, and the improvement of entrepreneurial R&D investment and the conversion rate of scientific and technological achievements can promote the number of entrepreneurs and entrepreneurial structure to different degrees. Effective predictions of the influencing factors and development trends of entrepreneurship in the future have been made, which provides policy references for entrepreneurship to be carried out more effectively in practice.