Under the guidance of the “dual carbon” strategy and the Sustainable Development Goals, improving ecological efficiency has become a key pathway for promoting China’s green transformation and high-quality development. This study aims to evaluate the spatiotemporal evolution of ecological efficiency and regional disparities across China. Using panel data from 30 provincial-level regions from 2012 to 2021, we construct an evaluation framework covering five dimensions: resource utilization, growth quality, green infrastructure, environmental governance, and ecological conservation. A unified assessment model is employed to measure provincial ecological efficiency, while Theil index decomposition and spatial autocorrelation analysis are used to examine temporal trends and spatial patterns. The results show that ecological efficiency in China has significantly improved over time, with regional gaps gradually narrowing. However, a persistent spatial pattern remains, characterized by high efficiency in the east, low efficiency in the west, rising levels in the central region, and fluctuations in the northeast. Intra-regional disparities are the main contributors to total variation, with greater heterogeneity in the eastern and western regions. Significant positive spatial clustering is observed in most years, with high–high clusters concentrated in central and eastern regions and low–low clusters prevailing in the west. These findings provide empirical support for regionally differentiated ecological governance and offer policy implications for advancing China’s green transition.