The compensation system for wildlife damage deviates from the concept of biodiversity protection, which should be corrected and improved in the context of speeding up the legal construction of biodiversity and implementing major projects for biodiversity protection. By outlining and describing the legislation system, logic and practice of the compensation system for wildlife damage, and from the perspective of biodiversity protection, we examine the compensation system for wildlife damage from the internal and external dimensions of the system. The study found that, on the one hand, authorized local legislation mode influences the construction compensation system for damage caused by the wildlife of completeness, and hard to the effectiveness of the security system, and the compensation scope and the integrity of the biodiversity protection concept differs markedly, on the other hand compensation system for damage caused by the wildlife and the biodiversity protection system to achieve cohesion, Forming a legal system for biodiversity protection. Future compensation system for damage caused by the wildlife should strengthen the legislation as a whole the compensation for the damage caused by the wild animals and to strengthen the place National People’s Congress to guide and supervise the compensation method development, expanding the scope of the damage caused by the wildlife protection and compensation legislation and promote biodiversity protection legislation to implement system cohesion, ensure biodiversity protection concepts rooted in implementation.