The invention discloses a compound podophyllotoxin gel for treating HPV virus and a preparation method thereof. The preparation method is characterized by including dissolving salicylic acid, phenol, acetoxychavicol acetate and podophyllotoxin in ethanol to prepare a solution, grinding the glycerin, carbomer 940 and azone uniformly in a mortar, adding dropwise triethanolamine slowly to form a gel, mixing the solution and the gel, and adding distilled water and stirring the mixture uniformly to obtain the compound podophyllotoxin gel. According to the invention, the solution is prepared from mixing salicylic acid, phenol, acetoxychavicol acetate and podophyllotoxin, the gel is prepared from adding dropwise triethanolamine into glycerin, carbomer 940 and azone, and the compound podophyllotoxin gel is prepared from mixing the solution and the gel and adding distilled water with stirring the mixture uniformly. The compound podophyllotoxin gel has an outstanding effect on treating HPV virus, and has high cure rate and low recurrence rate.