Abstract: The distribution automation terminals are widely applied in the medium-voltage distribution networks in China, while their program version management has got long-term attention. The core of this problem is the lack of consistency comparison methods of the terminal program versions. This article proposes a version consistency control mechanism of the distribution automation terminal program based on the DNA identification string. By constructing the feature factor vector model of the terminal program files and matching corresponding judgment priority and information abstract extraction algorithm, the core elements of the terminal program are first obtained. Then the core elements are filled into the base string as the valid data, and the data is masked to produce a DNA identification string, which has strong scalability and high anti-cracking capability. Further a method for the consistency comparison between the record of the standard sample DNA identification string and the tested sample is proposed, and a DNA string gene library and a testing database with hierarchical and block permissions are constructed. Finally, a sample test of the terminal programs sent to a certain city prove the effectiveness of the program version consistency control mechanism studied.