With the proliferation of unmanned aerial vehicles (UAVs), low-altitude networks are being utilized in various fields, such as smart cities and emergency response. However, their open wireless environment, dynamic topology, and resource constraints make them vulnerable to DoS attacks. To address these challenges, this paper proposes a Moving Target Defense (MTD) framework based on federated multi-agent deep reinforcement learning (FMADRL). We design lightweight and coordinated MTD mechanisms, such as leader switching, path mutation, and frequency hopping, to thwart attacks and enhance network resilience. Each UAV is equipped with a policy agent that autonomously selects MTD actions based on partial observations and local experience. Using a policy gradient-based algorithm, the UAVs jointly optimize policies through reward-weighted aggregation.