Abstract: In this paper takes coal cities as the research object, based on the concept of natural ecosystem and the characteristics of coal city, the evaluation index system of innovative ecological health degree of coal city is constructed from two aspects:innovative biological community and innovative environmental community.Using niche breadth and overlap model, the innovation ecological health degree of five coal resource cities in Shanxi Province from 2015 to 2019 is calculated and divided.Then, M estimation and intermediary effect model are used to study the influence of innovation ecological health degree of different types of coal resource cities on the collaborative agglomeration of coal industry and coal equipment manufacturing industry and the innovation driving effect of coal enterprises.The research show that Taiyuan City and Datong City are respectively innovative diversity, Changzhi City is innovative follow-up, Yangquan City and Jincheng City are innovative expertise, and different types of coal resource cities have positive effects on the collaborative agglomeration of industries.Among them, the technological innovation capability of coal enterprises has positive significance in the technological innovation of innovative and diverse cities.It is suggest that coal resource cities should be transformed into innovative and balanced cities, and the gap between cities should be narrowed.Enhance the technological innovation capability of coal enterprises, and steadily promote the collaborative agglomeration of coal industry and coal equipment manufacturing industry.