The Chinese government has adopted a significant low-carbon transition strategy aimed at enhancing resource efficiency, advancing ecological conservation, and augmenting societal well-being. This research employs the super efficiency SBM model to evaluate the ecological well-being performance (EWP) within the Huaihe River Ecological Economic Belt. Subsequently, it employs the Sys-GMM model and conducts a threshold effect analysis to regressively examine the impact of the low-carbon transition on EWP. The key findings are as follows. The EWP in the Huaihe River Ecological Economic Belt is relatively low; cities with higher economic development levels tend to exhibit lower EWP scores. The impact of the low-carbon transition on EWP is contingent upon the level of regional economic development and exhibits a singular threshold effect predicated on the economic development level as the threshold variable. Specifically, when economic development is at a low level, an intensification of the low-carbon transition results in a decline in EWP within the Huaihe River Ecological Economic Belt. Conversely, when the economic development level surpasses the threshold, the low-carbon transition facilitates the enhancement of EWP. This study’s principal contribution lies in elucidating the intricate relationship between the low-carbon transition and sustainable development.