The disclosure discloses a porcine epidemic diarrhea virus S protein and a subunit vaccine thereof as well as a method for preparing the subunit vaccine and application thereof. The vaccine contains 30˜220 μg of a recombinant porcine epidemic diarrhea virus S protein and a pharmaceutically acceptable ISA 201 VG adjuvant. A method for preparing the subunit vaccine comprises the following steps: (1) cloning the recombinant porcine epidemic diarrhea virus S protein； (2) expressing and purifying the recombinant porcine epidemic diarrhea virus S protein； (3) preparing the recombinant porcine epidemic diarrhea virus S protein prepared in (2) into a water phase； (4) emulsifying the water phase and the ISA 201 VG adjuvant in a volume ratio of 46:54 to obtain a vaccine. The vaccine is high in safety, good in immunogenicity, stable in batches, low in production cost and strong in immunogenicity. On the other hand, CHO cell strains suspending and stably and efficiently expressing the PEDV-S protein are successfully constructed and screened for the first time. The CHO cell strain can express the PEDV-S protein in high yield, the yield can reach 1 g/L, and the expressed PEDV-S protein is easy to purify.
