Academic entrepreneurial enterprises usually face the growth dilemma of small scale and slow growth. How to promote the growth of academic entrepreneurial enterprises is a key issue to be solved urgently in the context of China’s Innovation Driven Development Strategy. This study introduces the perspective of enterprise gene evolution, based on the longitudinal case of Neusoft Group, reveals the growth mechanism of academic entrepreneurial enterprises driven by gene evolution. The research has found that: (1) Academic entrepreneurial enterprises undergo the growth process of enterprise incubation stage, school enterprise collaborative development stage, and enterprise socialization stage, which is driven by the evolution of enterprise genes. (2) The genes of academic entrepreneurial enterprises will evolve under the combined influence of internal and external pressures, and the original genes will be replicated, mutated, and recombined to shift from academic orientation to academic & market orientation, and finally evolving into multi-integration enterprise gene. (3) Corporate genes influence the action selection of academic entrepreneurial enterprises around technology, opportunities, and resources, achieving a phased growth from enterprise incubation to expanding business scope, and then building a business ecosystem.