While scholars have explored the macro-macro linkages in entrepreneurial ecosystems (EEs) and how individual and organizational factors shape venture identity, this research examines how macro-level EEs influence the micro-level identity of new ventures, and how, in turn, ventures shape EEs that they belong to. Through a mixed-method approach that combines exploratory data analysis (EDA) of patent data and firm descriptions with comparative case studies in Beijing and Zurich, we find that market environments, institutional factors, ecosystem resources, and ecosystem actors guide ventures toward either a generalist or specialist identity. In dynamic, resource-limited contexts with competition like Beijing, new ventures tend to become generalists that serve multiple market segments and seize various opportunities, reinforcing a more diversified ecosystem. In more stable and resource-sufficient contexts like Zurich, new ventures develop niche specializations, strengthening the ecosystem’s focused expertise. By revealing the mechanism that EEs shape venture identity and new ventures as part of the internal dynamics of EE, we demonstrate that venture identity and EEs reciprocally interact in different contexts, bridging and contributing to the existing literature in key components and configuration of EEs and venture identity in entrepreneurship research. We also offer practical insights for entrepreneurs and ecosystem stakeholders who seek to foster supportive environments for new venture development.