Compulsory vaccination is an important policy for animal disease prevention. The“vaccination followed by compensation”is an important task of animal disease prevention and control departments. By reviewing the previous researches on the responsibilities of local governments and the relationship between central and local governments，and based on the principal-agent theory，a basic model of the relationship between central government or its departments and local governments，grass-roots governments or their departments as well as end clients was constructed under the industry management system，and the tension caused by inconsistent objectives and asymmetric information was analyzed. On this basis，the implementation mode of animal compulsory vaccination subsidy policy was analyzed，countermeasures and suggestions were put forward，and the common problems of public administration system in similar fields was discussed.