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Digital fountain codes can be applied into the file delivery in deep space communication for rateless and non-feedback characteristics. However, the code-length and typical sub-optimal algorithm are the two critical factors in deep space environment, which may guarantee the considerable decoding rate with power and buffer-limited equipment. In this study, a novel approach, dependent sequences compensation algorithm (DSCA) is proposed by restricting the randomness of fountain codes with code-length range of 103. Additional, the incremental Gaussian elimination to recover the data blocks in stopping set is also initialed. The simulation results show that 99.99% decoding rate with overhead under 0.20 and packet loss rate of 0.5 can be obtained with approach proposed in this study, which also indicate the usefulness of the new approach in the deep space communication systems.