With the diversification of the demand for auxiliary services in power system and the new form reconstructed by economic relations among related components of electric power system under new electricity reform, it is necessary to construct a reasonable auxiliary service cost compensation mechanism to adapt to special reforms of electricity auxiliary service market in the future. In this paper, the auxiliary service cost compensation mechanism is designed from five aspects, including the organization structure of auxiliary service supply subjects, the auxiliary service price mechanism, the basic operation forms of auxiliary service transaction, the risk prevention and allocation mechanism, and the policy guidance and supervision mechanism. On this foundation, the provision of incentive compensation for paid ancillary services, the new energy accommodation, cross-regional energy transmission and the problems of cost allocation among related subjects of electric energy storage is analyzed, and corresponding policy development suggestions are recommended for the compensation of auxiliary services and future marketization according to the economic and social benefits of cost compensation.