The invention discloses an SSD-oriented gene comparison method and a comparison system based on the same. The SSD-oriented gene comparison method mainly comprises the following steps: acquiring a first DNA fragment and a second DNA fragment, and aligning the two DNA fragments in SSD; reading the data of the two DNA fragments from the SSD, and determining comparison parameters according to the dataof the two DNA fragments and preset precision parameters; and based on the comparison parameters, performing progressive comparison on the two DNA fragments to obtain a comparison result. For the SSD-oriented gene comparison method, combined with the SSD, the data read-write frequency is reduced; and, the data is roughly screened by means of alignment, progressive comparison and the like, so thatthe proportion of the data needing to be edited for distance calculation is greatly reduced, and the efficiency is improved, and the calculation time is shortened.