Digital economy development (DED) empowers rural habitat (RH) improvement and promotes the construction of harmonious villages. Based on a panel data of 30 provinces in China from 2013 to 2019, this paper empirically tests the impact of DED on RH and its endogenous mechanism in multiple dimensions using panel fixed effects model and spatial Durbin model. The results show that DED significantly improves RH, which remains robust after a series of robustness tests and dealing with endogeneity issues. The mechanism analysis shows that DED helps to bring into play the rural resource allocation effect, the innovation and entrepreneurship effect, and the carbon emission reduction effect, and improves the RH through these three effects. Further study finds that the digital application divide and regional divide are the main barriers to digital technology enabling RH improvement, there is a spatial spillover effect of DED, which helps to promote the improvement of RH in neighboring areas. The results of the study can provide theoretical support and decision-making reference for the construction of digital villages and the balanced regional development of RH in China.