Urbanization is rapidly occupying green spaces, making it crucial to understand implicit conflicts between urbanization and greenness. This study proposes an ecological greenness index (EGI) and a comprehensive urbanization index (CUI) and selects Nanjing, a megacity in China, as the study area to research the spatial and temporal evolutionary trends of the EGI and CUI in the context of land use/land cover (LULC) changes from 2000 to 2020. Meanwhile, the conflicts and complex interaction characteristics of the EGI and CUI are discussed from both static and dynamic perspectives, and their driving mechanisms are investigated by combining specific indicators. The results demonstrate that over the past 20 years, LULC in Nanjing was dominated by cultivated land, forest land, and artificial surfaces. The encroachment of artificial surfaces on green space was strengthened, resulting in a decrease in the proportion of cultivated land from 70.09% in 2000 to 58.00% in 2020. The CUI increased at a change rate of 0.6%/year, while the EGI showed significant browning (change rate: −0.23%/year), mainly concentrated within the main urban boundaries. The relationship between the CUI and EGI made the leap from “primary coordination” to “moderate coordination”, but there remains a risk of further deterioration of the decoupling relationship between the CUI and ecological pressures. The multi-year average contribution of the CUI to the EGI was 49.45%. Urbanization activities that dominate changes in greenness have changed over time, reflecting the timing of urban conflict management. The results provide important insights for urban ecological health monitoring and management.