The invention provides a referential DAN sequence compressing method and system. The method comprises the step of matching repeated patterns, namely, creating an inverted full-text subsequence structure based on an input reference sequence, and performing the longest matching subsequence searching on the input sequence to be compressed, wherein the matching information is applied to the compressed encoding step, and the unmatched symbols are applied to the step of predictive encoding of non-repeated symbols; the step of compressed encoding step, namely, performing compressed encoding on the matching sequence length and location information, wherein the encoding information is applied to decompressing; the step of predictive encoding of non-repeated symbols, namely, receiving unmatched symbols in the step of matching the repeated patterns, and predicting the symbol occurrence probability and encoding through a mixed context model. According to the method, the properties of efficient searching of index data and efficient compressing of the mixed context model to single symbol are fully combined, so that when being compared with that of other referential DNA sequence methods, the compressing rate is high within the acceptable compressing time consumption; the method is high in practicability.