Regional carbon emission efficiency has differentiated characteristics under different economic development stages and patterns, and it is significant to identify such characteristics and formulate corresponding policies for high-quality regional development. Based on input-output data related to economic development and energy consumption, a comprehensive evaluation model of Super-SBM and Malmquist-Luenberger (ML) index was constructed to evaluate the spatial and temporal changes and driving forces of CEE, on the basis of which a proposal for collaborative carbon emission reduction zoning is proposed. The results indicated that the carbon emission efficiency (CEE) of the YRD shows a fluctuating upward trend with obvious spatial agglomeration characteristics, and the changes in CEE were closely related to the stage of economic development. The annual average CEE value during each period exhibited positive changes, indicating that economic development gradually shifted toward low carbonization. Moreover, the improvement of CEE gradually shifted from being driven by efficiency change to being driven by technological change. Finally, based on the carbon emissions and CEE characteristics of different cities, a carbon-neutral synergistic path is proposed in terms of industrial transformation, green development and technological support.