The invention relates to a gel preparation for treating gynecological diseases. The gel preparation consists of chitosan with specific molecular weight and degree of deacetylation, chlorhexidine, glycerin, an acidifying agent and purified water. The preparation method comprises the following steps of: mixing the chitosan with the purified water to form suspension liquid in an environment with cleanliness at one-hundred-thousand level; adding the acidifying agent to regulate pH to 3.8-5.8 to obtain chitosan gel; dissolving chlorhexidine in the glycerin, adding into the chitosan gel, uniformly stirring, degassing, filling, sealing, and sterilizing to obtain the gel preparation, wherein the acidifying agent is lactic acid, acetic acid or a hydrochloric acid-acetic acid mixture; and the sterilizing mode is cobalt-60 irradiation treatment or high-temperature damp-hot sterilization. The gel has good adhesion force, uniform color and good stability, is used for treating women monilial vaginitis, bacterial vaginitis, mixed vaginitis, cervicitis, cervical erosion and the like, and has the advantages of being good in curative effect, safe, natural, good in biocompatibility and the like. The invention further relates to a preparation method and medical application of the gel preparation.