Digital fountain is applied into deep space communication for its rateless and non-feedback forward error correction.However,the long code length and encoding overhead are confined factors to guarantee a considerable recovery probability as power and buffer-limited equipment in deep space environment.At the same time,the typical fountain decoding is sub-optimum decoding algorithm.We propose a new approach,Dependent Sequences Compensation Algorithm (DSCA),to improve the encoding efficiency by restricting the randomness in fountain encoding.While decoding algorithm is also optimized by redundant information in stopping set.The results show that the optimized method can obtain a 10-4 decoding failure rate with overhead under 0.20 for code length 500,which indicates the usefulness of the proposed approach in deep space communication.