How can enterprises acquire knowledge resources quickly to maintain a competitive advantage in the market has become the focus of attention among academic circles and enterprises in the era of the knowledge economy. Based on the ecology theory, this paper analyzed the characteristics of the innovation subject and the rules of the heterogeneous knowledge interaction between innovation subjects. Then, this paper proposed a multiagent‐based model of EIE (enterprise innovation ecosystem) heterogeneous knowledge increment to simulate the interactions between innovation subjects. By combining the biotic factors (government and service institutions) and abiotic factors (economical, social, and cultural), this paper designs eight different innovation environment scenarios to explore the dynamic impacts of these factors on EIE heterogeneous knowledge increment. The research findings were as follows: (1) In the introduction stage of innovation collaboration between innovation subjects, the same investment of the innovation elements in academic institutes is more beneficial to increasing system heterogeneous knowledge than investment in enterprises. (2) The cultivation of innovative biotic factors in service institutions is conducive to the rapid interaction of heterogeneous knowledge among the innovation subjects. Still, it is not suitable for areas with higher homogeneous knowledge because high homogeneous environment can easily lead to intensified market competition. (3) The cultivation of the abiotic innovation environment is conducive to maintain stable high‐speed growth of EIE heterogeneous knowledge increment over a long period. (4) Without considering the cost of environmental cultivation, cultivating biotic and abiotic environments at the same time is the most beneficial choice to EIE heterogeneous knowledge increment.