Improving the ecosystem quality (ESQ) is a major requirement for national ecological civilization construction and the ultimate goal of the ecological restoration project. However, the assessment of ecosystem function, health and quality was based on actual values of the ecological indicators dominated by climate in previous studies, and the comparability of evaluation results between different regions was too low to meet the needs of national ecosystem management. In this paper, based on a reference system-based ecosystem quality assessment framework and 168 assessment units divided by China's eco-geographical zones and vegetation types, we used ecosystems that were less disturbed by human activities and had excellent ecosystem structure and functions, such as the core area of the National Nature Reserve, the permanent observation plots of the Chinese Ecosystem Research Network (CERN), and areas where productivity was mainly affected by climate as reference benchmarks, and estimated China's terrestrial ecosystem quality based on reference system (ESQ') and its changes during 1990—2015. The results show that the average value of China's terrestrial ecosystem quality index was 28% lower than that of the reference ecosystem. China's ESQ' decreased by 1.2% during 1990—2000 and increased by 3.69% during 2000—2015, respectively. The regions with obvious transformations were mainly distributed in the Shaan-Gan-Ning loess plateau hilly and gully water and soil conservation ecological function zone, Changbai Mountain and counties in the southwest of the rocky desertification control project. Ecological restoration projects such as the Grain for Green Project, shelter forests and comprehensive control of rocky desertification in these regions have played an important role in improving the structure, function and stability of the ecosystem, thereby promoting the improvement of ecosystem quality. The method of ecosystem quality assessment based on reference system can eliminate the impact of differences in climate conditions on the quality assessment between different regions to a certain extent, provide a feasible new way to quantify the impact of human activities on the ecosystem, and provide references for China's ecosystem management and land use management. We suggest that the government should strengthen the networked observations of reference ecosystems in different ecological geographic regions and different vegetation types of China in the future, and focus on the impact of future climate change and the trade-off relationship between ecosystem functions on ecosystem quality.