The entrepreneurial ecosystem is of great significance for the innovative growth of new startups. Based on the symbiotic perspective of entrepreneurial ecosystems, dynamic QCA was used to conduct configuration analysis on 30 provincial cases, exploring the complex causal mechanism of entrepreneurial ecosystems driving innovation performance of new startups. Research has found that: (1) No single factor can achieve high innovation performance in new startups. (2) There are five paths that lead to high innovation performance in new startups, which can be classified into three categories: “environment driven”, “factor flow driven”, and “industry network environment balance driven”; There are 9 paths that generate non high innovation performance for new startups. (3) There is a significant time effect in each configuration, and after 2019, the consistency level of each configuration is relatively high and tends to stabilize. The institutional environment has always been in a stable state and played an important role, while the entrepreneurial ecosystem has evolved from the “construction stage” to the “self-organization stage”, with “industrial structure+financial capital” playing a key role. (4) There are significant differences in the paths through which regions with different levels of development drive the innovation performance of new startups. (5) There is an equivalent substitution effect between the symbiotic matrix and the symbiotic network. The research conclusion provides reference for improving the innovation performance of regional new startups.