Innovation and entrepreneurship, as an important part of social and economic activities, has received more and more widespread attention. Based on the characteristics of the digital era, the study uses artificial intelligence to empower innovation and entrepreneurship education in colleges and universities. Optimize the allocation of innovation and entrepreneurship education resources in colleges and universities through multi-objective optimization algorithm. Construct an optimization model of resource allocation for innovation and entrepreneurship education in colleges and universities, and verify its resource optimization and allocation performance. Taking 13 colleges and universities in C city as the research object, the optimization of their innovation and entrepreneurship education resource allocation is processed. The MSS cumulative values of this paper’s multi-objective optimization model on the CPLX problem and the MATP problem are -1.400 and -1.033, respectively, which are the smallest among all models, with the best performance and ranked the first in resource allocation efficiency. After optimization, the resource allocation level of innovation and entrepreneurship education in all 13 colleges and universities has been improved, and the resource allocation among the colleges and universities is more balanced.The resource utilization efficiency of innovation and entrepreneurship education in the 13 colleges and universities has been improved by 17.02% on average.