In the context of China’s 2020 dual carbon goals of peak CO2 emissions by 2030 and carbon neutrality by 2060, the security of multi-energy systems is increasingly challenged as clean energy continues to be supplied to the system. This paper proposes a risk assessment and enhancement strategy for distributed energy stations (DESs) based on a security boundary. First, based on the coupling relationship between different energy sources and combining the mutual support relationships between different pieces of equipment, a security boundary for DESs was constructed. Second, based on the characteristics of different sources of equipment failure, the real-time failure probabilities of equipment and pipelines were calculated in order to obtain the security risks of DES operation states based on the security boundary. Finally, for equipment and pipelines at high risk, an economic security enhancement strategy is proposed, and the Pareto solution set is solved using a multi-objective algorithm. The analysis shows that the proposed method can effectively quantify the security risks of energy systems in real time, and the proposed enhancement strategy takes into account both economics and system security.