The Yangtze River Economic Belt (YEB) and the Yellow River Ecological Economic Belt (YREB) surround the two biggest inland rivers and emit the greatest amount of carbon emissions in China. In order to implement China’s dual carbon goal, this research applies a Meta-frontier DN-DEA model, including the carbon reduction factor (CRF), to assess the emission efficiency of energy, CO2, and atmospheric pollutants for a total of 19 regions in YEB and YREB from 2011 to 2017. The synergistic climate risk control efficiency of atmospheric pollutants in the two economic belts are verified by tests for CO2 and three atmospheric pollutants emission elasticity coefficient and Kendall’s coordination coefficient. The results are as follows: First, the overall efficiencies of the two economic belts are both improved by over 30% when subject to CRF. YREB has great potential for carbon emission reduction, and the growth rate of its overall efficiency is higher than that of YEB. Second, YEB’s input term efficiency performs better affected by CRF, while YREB’s environmental pollution control input is insufficient. Third, CO2 and atmospheric pollutants emission efficiencies are significantly improved in YEB, while the environmental regulation of YREB is not obvious for the climate co-benefit of CO2 and atmospheric pollutants. Lastly, high level of climate co-benefit has revealed in YEB during 2011 to 2016, while in 2017 it plummets sharply. Conversely, YREB maintains a stable climate co-benefit.