Current Unmanned Aerial Vehicle (UAV) swarm designs prioritize physical reliability over network security, leaving systems vulnerable to increasingly sophisticated cyber threats in complex environments. Existing defense methods are mostly limited to peripheral network security technologies, such as encryption, authentication, and firewalls. Consequently, they lack deep integration at the formation architecture level. This separation results in a disconnect between system reliability design and security protection mechanisms, making it difficult to effectively deal with high-level security threats such as internal backdoor vulnerabilities. To this end, this paper proposes an endogenous security architecture for UAV swarm based on dynamic heterogeneous redundancy (DHR) and cooperative supervision. Firstly, a theoretical model of DHR system for UAV swarm was constructed, and discrete nodes are abstracted as dynamic heterogeneous resource pools. Through the formal definition of the heterogeneous executor space, redundancy adjudication mechanism, and dynamic scheduling method, we demonstrate how this architecture suppresses common mode failures by introducing internal and external uncertainties, thereby realizing the coordination and unification of safety and security. Secondly, a distributed security control strategy based on cooperative supervision is proposed, which uses cross-validation between neighbors to replace the centralized adjudication of traditional DHR, solves the problem of anomaly detection in a decentralized environment, and combines reactive cleaning and periodic disturbance scheduling to give the system the ability to self-heal against unknown threats. Simulations in various attack scenarios demonstrate the proposed method’s superiority over traditional architectures. Especially in the simulated dormant multi-mode Advanced Persistent Threat (APT) scenario, the system can still maintain availability of more than 81%, which effectively verifies the key role of the coordination mechanism of heterogeneity, redundancy and dynamics in enhancing the safety and security of UAV swarms.