In environments with unknown communication interference, the mission efficiency of heterogeneous unmanned aerial vehicle (HUAV) swarms is often impacted by communication disruptions due to regions of strong interference encountered when executing reconnaissance and coverage missions. Existing research has rarely focused on communication interference or on the differences in HUAV characteristics under various control architectures; thus, in this paper we explore the performance differences between HUAV swarms based on centralized, distributed, and centralized-distributed architectures when executing reconnaissance and coverage missions in environments with unknown communication interference. First, a communication model in an unknown interference environment is constructed to reflect the real-time communication status of the swarm. Second, in response to the limitations of the traditional artificial potential field (APF) algorithm in this environment, a coverage-oriented artificial potential field (COAPF) algorithm is proposed. Finally, based on the COAPF algorithm, a multi-dimensional comparison of the mission completion efficiency of HUAV swarms with three different architectures is conducted. Our simulation results indicate that the distributed architecture is suitable for large-scale environments with strong interference, while the centralized–distributed architecture performs better in small-scale environments with weak interference. Conversely, the centralized architecture exhibits poor performance in all interference scenarios due to its lack of decision-making capabilities.