Non-cooperative unmanned aerial vehicles (UAVs) equipped with array antennas are able to recognize the directions of the arriving signals. Traditional GNSS spoofing transmits signals from one single antenna, which are easy to be detected, recognized and mitigated by such UAVs. To address this problem, we propose a distributed covert GNSS spoofing method that utilizes cooperative UAVs with spoofing payloads to transmit spoofing signals from various directions. This approach effectively offsets the signals arriving directions recognition capability of the array antennas. Meanwhile, a novel hybrid clustering algorithm is introduced to optimize the deployment location of cooperative UAVs, so that the spoofing signals’ arriving directions are closer to those of the real signals. The results of field experiments validate the covertness and feasibility of the proposed methods.