Unmanned aerial vehicles (UAVs) confront various interference in the process of missions, and frequency hopping (FH) technology is one of the effective means of anti-interference for UAV. The FH system can avoid interference frequency points and possess certain anti-interference ability by making the carrier frequency continuously popping. However, the increasingly complex electromagnetic environment of UAV swarms requires more efficient anti-interference measure. To further improve the anti-interference ability of UAVs, this paper proposes a cognitive-based high robustness FH strategy. By adding a cognitive module to FH system, UAVs can avoid the interference frequency points adaptively and sensitively. The proposed system can identify typical suppressed interference and filter the interference frequency points. Cognitive FH system can avoid interference points completely with accurate detections and enhance the robustness for UAV swarms in complex electromagnetic environment compared to conventional FH system. Simulation results have shown that BER performance of proposed cognitive FH strategy is better than conventional FH strategy for typical suppressed interference.