The invention innovatively provides an application of a novel base conversion editing system on gene therapy for the first time; according to the system, the function of a single-base gene editing system is reserved, which is characterized in that conversion from C / G to T / A of a single base at a specified site is realized, conversion from A / T to G / C is realized, and the conversion from C / G to T / Aand from A / T to G / C can be also realized. The basic group conversion editing system comprises sgRNA, nuclease, cytosine deaminase, adenosine deaminase and uracil glycosidase inhibitors, and the nuclease, the cytosine deaminase, the adenosine deaminase and the uracil glycosidase inhibitors can target and recognize DNA sequences. The invention further provides a pharmaceutical composition containingthe base conversion editing system and the application of the pharmaceutical composition in gene editing, gene therapy, drug screening and model animal construction.