The proliferation of UAVs has enabled a wide range of mission-critical applications and is becoming a cornerstone of low-altitude networks, supporting smart cities, emergency response, and more. However, the open wireless environment, dynamic topology, and resource constraints of UAVs expose low-altitude networks to severe DoS threats. Traditional defense approaches, which rely on fixed configurations or centralized decision-making, cannot effectively respond to the rapidly changing conditions in UAV swarm environments. To address these challenges, we propose a novel federated multi-agent deep reinforcement learning (FMADRL)-driven moving target defense (MTD) framework for proactive DoS mitigation in low-altitude networks. Specifically, we design lightweight and coordinated MTD mechanisms, including leader switching, route mutation, and frequency hopping, to disrupt attacker efforts and enhance network resilience. The defense problem is formulated as a multi-agent partially observable Markov decision process, capturing the uncertain nature of UAV swarms under attack. Each UAV is equipped with a policy agent that autonomously selects MTD actions based on partial observations and local experiences. By employing a policy gradient-based algorithm, UAVs collaboratively optimize their policies via reward-weighted aggregation. Extensive simulations demonstrate that our approach significantly outperforms state-of-the-art baselines, achieving up to a 34.6% improvement in attack mitigation rate, a reduction in average recovery time of up to 94.6%, and decreases in energy consumption and defense cost by as much as 29.3% and 98.3%, respectively, under various DoS attack strategies. These results highlight the potential of intelligent, distributed defense mechanisms to protect low-altitude networks, paving the way for reliable and scalable low-altitude economy.