A channel estimation algorithm based on subspace structured covariance is proposed in this paper for the pilot contamination problem of distributed massive MIMO systems.The algorithm utilizes the spatial location characteristics of the distributed massive MIMO systems and performs the pilot contamination elimination based on the non-overlap characteristics of the delay-Doppler-angle domain channel supports.Then,a pilot assignment scheme is also designed in this paper for the proposed algorithm to reduce the impact of overlapping channel supports on the pilot contamination elimination performance.The theoretical demonstration and simulation analysis show that the proposed algorithm has better performance than the representative baseline scheme.