Flight data is a typical time series whose random noise and complex deformation cause the difficulty of sub-sequence similarity query. For this reason, a similarity query method for flight data time series sub-sequences based on pathologic matching of DTW is proposed. Firstly, boundary curves are built up and down by using query sequence sample sets. Simultaneously, lower bounding distance is proposed with a proof correctness to build lower bounding algorithm for filtrating subsequences to increase efficiency. Then, the invalid subsequence field is recognized and deleted for determining the valid subsequence field of matching by pathologic matching of DTW. The results show that the proposed method can accurately find similarity sub-sequences，and the start stop time deviation can be controlled in less than 3 seconds, meeting the actual needs of aircraft flight action query.