Enhancing carbon emissions efficiency (CEE) is one of the effective ways to improve ecosystem services (ESs) and achieve sustainable developments. For Yangtze River Economic Belt (YREB), China, achieving better CEE is essential after three decades of developments. This would require an integrated understanding of the relationship between CEE and ESs, which is spatially explicit. This study analyzed multi-source data between 1990 and 2020 in YREB with consideration to the spatial relationships between CEE and total ecosystem services (TES) and the spatial spillover effects of CEE. By adopting a spatial econometrics method, it further analyzed the spatial response mechanism between CEE and TES, which is important for developing sustainable land use strategies and managing ecosystems. The analyses showed that food productivity (FP), carbon sequestration and oxygen production rate (CSOP), water retention (WR), and soil conservation (SC) increased from 1990 to 2020. Moreover, the maldistribution of water systems and the difference in coverage of cultivated land and forestland together led to different spatial distributions of TES in YREB–a high TES cluster in the east and gradual decrease of TES toward the west. CEE throughout the region showed a slight upward trend, with the highest CEE exhibiting a congregated pattern in the middle and lower reaches. The overall spatial correlation between CEE and TES is significantly negative, and CEE has significant spatial spillover effect on TES, meaning that increased CEE in a specific region will lead to degraded TES in neighboring regions, which also presented empirically-supported recommendations for optimizing land use zoning and fostering sustainable development at a regional scale. And the study provides concrete evidence that TES is determined not only by CEE in-situ, but also surrounding regions. Therefore, the spatial negative spillover effects of CEE should be fully considered in the formulation of sustainable development policies, specifically in inter-regional cooperation.