To provide effectively basic support for China’s development of ecological civilization, this paper focuses on the research interests of ecological problems, identifies the ecological problems of different ecoregions, and proposes the directions of ecological protection and restoration. The methods used in this paper include research interest evaluation model, comparative analysis method and inductive summary method. The results show that 1) Since 1980, the research interest on ecological problems in China has shown an overall trend of growth. After 1998, the research interest on ecological problems entered an accelerated period, and a new round of research on ecological civilization started in 2012. As China has gradually realized the importance of ecological protection, the research on ecological problems in China has been enriched from theoretical system, technical methods to practical application. 2) there are obviously internal and spatial differences in the research interests of ecological problems in China. The ecological problems with high research interest are soil erosion and biodiversity loss, more than 85% of cities have carried out academic research on these two ecological problems. In addition, the research interest of ecological problems presents spatial aggregation characteristics, and the hot areas are concentrated in the western China. 3) Soil erosion, desertification, biodiversity loss, and degradation of forest, grass and wetland ecosystems are the ecological problems that each ecoregion focuses on. More than half of the ecoregions focus on the degradation of forest ecosystems, while ecological problems such as rocky desertification, salinization and degradation by mining are concentrated in fragile ecoregions. In addition, more than 80% of the ecoregions have more than three major ecological problems, which reflects the urgency and complexity of China's ecological problems. 4) There are differences in the direction of ecological protection and restoration in the ecological region. Ecological regions with good ecological status and few human activities focus on conservation and natural restoration, and the ecological protection and restoration of such ecoregions should focus on the establishment of protected areas, breeding and reproduction of endangered species, and strengthening the monitoring of biodiversity. Agro—ecological region with a generally ecological status or the eastern tropical and subtropical ecological forest region mainly focuses on natural restoration and auxiliary regeneration, and the measures of ecological protection and restoration include natural enclosure, artificial afforestation and grass planting, agro-forestry, etc. Ecological regions with fragile habitats and frequent human activities focus on auxiliary regeneration and ecological reconstruction, and engineering, physical, chemical and biological restoration measures should be promoted in such ecoregions. In conclusion, there are obvious differences in ecological problems in China. An accurate understanding of the types, severity and occurrence mechanism of ecological problems in different ecoregions is a prerequisite for carrying out ecological protection and restoration work on territorial space.