In China, researches on ecological compensation should be dated back to the 1980s’ when the discussions on ecological compensation in ecological and economic senses were initiated. Since the United Nation′s Conference on the Human and Environment in 1992, ecological compensation researches have entered into a phase of theoretical discussions on “damager pays” principle. With the implementation of ecological protection programs and the reorganization of conflicts between ecological protection and economic development, ecological compensation researches have paced into a phase of theoretical and practical discussions with special emphasis on “beneficiary pays” principle. Nowadays, ecological compensation has been a hot-spot in all walks of Chinese society. While the key scientific issues in ecological compensation research, such as connotation, standard, approach, implementation mechanism and theoretical basis, etc remains unsolved. Connotations of ecological compensation in China have been moving from emphasizing on ecological senses to economic senses. The clarification of the relationships between ecological fees, environmental fees and resource fees is a key for implementation of ecological compensation mechanism. It is recognized that the basic principle of environmental economics, or externality theory and public goods theory, could be considered as the basis for ecological compensation research. And the consideration of ecosystem services as the basis for compensation is dependent on the controversy of compensation for the benefits or for the values. Determination of eco-compensation standards is at its early stage, and the current research involves the elements such as quantitative assessment of ecosystem services, opportunity cost, demand and supply analysis, etc. The resolution of aforementioned issues is critical for ensuring feasibility and validity of eco-compensation mechanism and its successful implementation, which calls for integration of theoretical and practical researches with association of the Chinese situation and within regional specific challenges. The paper suggests that the future research should focus on, but not limited to, the following perspectives: (1) definition of terminology of ecological compensation with consideration of regional requirement; (2) study on theoretical basis and calculation of eco-compensation standard based on practical validity; (3) eco-compensation mechanism with participation of stakeholders; (4) integrated research on ecosystem service and ecological compensation mechanism.