A method and a system for reoptimizing unmanned aerial vehicle formation communication topology based on minimum cost arborescence are used for optimizing reconstructed UAV formation communication topology after a communication failure occurs on the UAVs in the formation. The method includes calculating a first communication cost of the reconstructed UAV formation communication topology; comparing the first communication cost with a target communication cost for the minimum cost arborescence of the formation communication diagram under a predetermined state; when the first communication cost is greater than the target communication cost for the minimum cost arborescence of the formation communication diagram under the predetermined state, optimizing the reconstructed UAV formation communication topology through a predetermined strategy.