Since the 1990s, miscellaneous ecological protection programs, particularly ecological compensation policies and engineering projects have been implemented globally. Especially after the 1998 Yangtze River flood, China implemented a series of ecological compensation policies and engineering projects, including the Natural Forest Conservation Program, Grain to Green Program, Beijing-Tianjin Sandstorm Control Program, Forest Ecological Benefits Fund, Conversion of Croplands to Wetlands Program, and Ecological Transfer Project. Recently, government officials, researchers, and other stakeholders have been paying more and more attention to the ecological and socioeconomic outcomes of those ecological protection programs. Nevertheless, impact evaluation of ecological protection programs in China is only at its initial stage, mainly due to insufficient quantification, poor research design, unreasonable baseline selection, oversimplified evaluation methodology, weak causal inference, and poor credibility of evaluation results. Therefore, it is urgent to promote impact evaluation of ecological protection programs in China from both the academic and national strategic perspective. To achieve this goal, based on theoretic and empirical experience over the past decade, we synthesized problems and challenges on the impact evaluation of ecological protection programs, ranging from the research design, baseline establishment, and evaluation methods.