Currently, numerous rural regions face the dual challenges of energy poverty and environmental pollution, which highlight the urgent need to improve the clean energy consumption structure in these areas. Against the backdrop of digital development, this study employs a series of exogenous treatment effect models to estimate the impact of e-commerce on the transition to clean energy in rural areas and explore its underlying mechanisms using agricultural census big data from China. The results indicate that the adoption of e-commerce can significantly facilitate the transition to clean energy, which remains robust even after addressing endogenous issues. Specifically, villages equipped with an e-commerce delivery station experience a 25% to 41.33% improvement in their natural gas connection rate compared to villages without such facilities. Heterogeneity analysis reveals that the impact of e-commerce on promoting clean energy transition is more pronounced in villages located in the underdeveloped western and highland regions, as well as those with public transportation systems and village secretaries who have education levels below high school. Furthermore, as the likelihood of a village participating in e-commerce decreases, the impact of e-commerce on the clean energy transition strengthens. Lastly, the underlying mechanisms suggest that e-commerce contributes to the transition towards clean energy by strengthening collective action, promoting rural commerce development, and increasing participation in pension insurance. These findings suggest that promoting e-commerce development in rural areas is a crucial strategy for effectively driving energy transition, especially in underdeveloped rural areas.