Chongyi Hakka Terrace is located in Chongyi County in the south of Jiangxi Province, which is the largest Hakka Terrace in China. As a special agricultural ecosystem, it provides many ecological services for the Hakkas in Chongyi County. In recent years, with the increase in the opportunity cost of rural labor output, the abandonment of Chongyi Hakka terraces is becoming more and more serious, and the sustainable development of its ecosystem is facing severe challenges. Therefore, it is necessary to build a reasonable ecological compensation mechanism to promote farmers’ protection of the terrace ecosystem in the Chongyi Hakka Terrace area. In this paper, the problems existing in the Chongyi Hakka Terrace ecosystem are analyzed, and the externality of economic benefits and the subject and object of ecological compensation of the Chongyi Hakka Terrace ecosystem are identified. Based on this, combined with the existing research results, the ecological compensation standard of the Chongyi Hakka Terrace system is formulated, the government should provide 6.58×10⁸ RMB·per year to farmers in the large-scale contiguous area of Chongyi Hakka Terrace. The priority of ecological compensation of the three townships in the large-scale contiguous area is Sishun Township, Fengzhou Township, and Shangbao Township. At the last, the implementation system of ecological compensation for the Chongyi Hakka Terrace system is proposed, for the purposes of providing a reference for government departments to formulate sustainable management countermeasures for the Chongyi Hakka Terrace ecosystem.