In the last decades, many ecological conservation and restoration projects have been carried out and significant achievements have been made in China. However, many of these projects took the single element and single type of ecosystem, such as wetlands, forests, and grasslands etc. as the conservation and restoration object, lacking the overall and systematic consideration at regional scale. From the perspective of a complete watershed, holistically ecological conservation and restoration projects of mountains, rivers, forests, farmlands, grasslands, and deserts have been launched out at landscape scale since 2016, based on the concept that mountains, rivers, forests, farmlands, lakes, and grasslands are a community of life. For these projects, the integrity of the ecosystem, the continuity of the physical geography unit and the socio-economic sustainability were systematically considered. These projects contained relatively complex goals and tasks of conservation and restoration. Thus, the following challenges e.g. multiple sub-project types, multiple spatial scales, multiple targets, and short implementation period etc., might be faced in effectiveness evaluation. As for the spatial scale, the targets of evaluation should cover both relatively large and certain range of space, which have always been set in conventional evaluation, as well as conservation and restoration unit (the ecosystems generally face the similar problem and share similar objectives) and sub-project (the specific conservation and restoration measures are taken). As for the temporal scale, both the effectiveness at the end of project implementation and the effectiveness dynamics after the end of implementation should be taken into consideration. As for the content of evaluation, it should not only focus on the social, ecological, and economic benefits, but also investigate the relationship between the engineering measures and ecological effects, the correlation and synergy of different types of sub-projects, and the integrity and systematization of the project. Based on the above background, a novel evaluation framework was built in the current study, as the traditional evaluation could not meet the technical and management requirements. In this framework, the index system based on three scales (sub-project, conservation and restoration unit, and scope of project) and the evaluation content including four aspects (ecological, social and economic benefits and management effects), were emphasized. The novel framework would help improve the standard system of holistically ecological conservation and restoration project of mountains, rivers, forests, farmlands, grasslands, and deserts, and provide technical support for promoting the overall conservation, systematic restoration, and comprehensive management of territorial space in China.