Based on the theory of dissipative structure， it explored the entropy change of regional innovation ecosystem caused by the environment. From the perspective of ecology， an environmental effect index system of regional innovation ecosystem was proposed， and the evaluation model of environmental effect of innovation ecosystem was constructed based on the Brusselator translation model. An empirical study was conducted with different regions divided by 29 provinces in China as the research objects. The results show that： the entropy of environmental effects of regional innovation ecosystems shows an upward trend， and the negative entropy in the eastern region is significantly higher than those in the central and western regions； most regions with strong environmental effects of regional innovation ecosystems are located in eastern China； disparities in environmental effects of regional innovation ecosystems have been intensified. From 2012 to 2017， the overall Gini coefficient and the Gini coefficients of the three regions and between the three regions have increased. Intraregional disparities gradually become the main source of total disparity. The spatial agglomeration of environmental effects is not significant. Based on the results of empirical research， it put forward the following policy suggestions： adjust the policy direction according to the index entropy weight of negative entropy of environmental effects， narrow the regional disparities of environmental effects， and enhance the regional radiation function of regional innovation ecosystems environmental effects.