Medical insurance payment reform affects physicians’ clinical decision-making through hospital management. Drawing on principal–agent theory and behavioral economics, this paper constructs an institutional incentives–organizational transmission–behavioral responses framework to explore the mechanisms of DRG/DIP reform. Payment rules alter hospitals’ revenue and risk constraints and, through performance assessment, intra-hospital risk sharing, medical record quality control, and digital supervision, shape physicians’ reference points, risk perceptions, and professional autonomy. Physicians’ responses are examined along three analytical dimensions: standardized response, strategic adaptation, and formal compliance. Practices in Shanghai and Huaibei provide illustrations at the institutional and organizational levels through organizational goal transformation and the linkage of risk compensation; transmission to clinical behavior remains to be empirically tested. The analysis identifies organizational transmission as a key link between payment incentives and clinical behavior. It recommends compensating reasonable costs, improving quality-oriented performance assessment, verifying medical record authenticity, and providing feedback through clinical review to promote alignment between payment incentives and clinical value.