Background: This study develops a multi-level model of healthcare alliance (HCA) formation in Taiwan’s healthcare sector. We focus on how industry-level environmental factors stimulate government-level institutional changes, ultimately shaping healthcare organizations’ (HCOs) decisions to form HCAs. Methods: A qualitative case study was conducted to explore ten dyadic HCAs. In-depth interviews with 25 key informants were analyzed using a mixed-methods approach, combining in-depth interviews with a theoretical framework of alliance development. Results: Findings reveal a multi-level understanding of HCA formation. Market and technology turbulence drive HCOs to form HCAs for cost reduction and resource development. Government institutional changes, influenced by the pandemic, further motivate HCA formation for legitimacy. However, government-led HCAs prioritize institutional factors, while HCO-led HCAs focus on transaction cost factors and resource-based factors. Conclusion: This study contributes to the literature by integrating theories of transaction cost economics, resource-based view, and institutional theory within the healthcare context. It highlights the importance of a multi-level perspective to understand HCA formation and provides practical implications for healthcare leaders and policymakers.