Abstract: The rapid development of the low-altitude economy and the continuous release of policy dividends posed severe challenges to the airspace regulatory system. To address this challenge, a dynamic game model of bounded rationality between the government and logistics enterprises was constructed based on evolutionary game theory. By setting parameters such as government enforcement costs, enterprise compliance and violation costs, policy incentives, penalties for violations, risk losses, social benefits, and enterprise revenues, the replicated dynamic equations for the strategy choices of both parties were derived. Combined with local stability analysis, the possible equilibrium states of the system and the influence mechanisms of key parameters were explored. It is found that excessive penalties may instead encourage enterprises to violate regulations; merely improving regulatory efficiency is insufficient to enhance compliance rates, requiring policy coordination; compared with strengthening penalties or regulatory intensity, curbing enterprises’ illegal gains or increasing compliance subsidies is more effective in promoting compliance. The conclusions indicate that the strategy evolution of governments and enterprises is jointly influenced by multiple parameters, and the design of policy tools should emphasize synergy and differentiation. This study provides a theoretical basis for low-altitude economic regulatory policies that balance safety bottom lines and development vitality.