This study analyzes the role of digital village construction in enhancing agroecological efficiency (AEE) in China, emphasizing its impact on rural governance, including bureaucracies, self-governance bodies, market forces, and social organizations. Using data from 30 provinces (2014–2020), the research explores the dynamics and diversity of multi-level governance in improving AEE. Key findings include a significant positive correlation between digital villages and AEE, though this relationship weakens in an "inverted U" pattern beyond a digital development index of 0.8. Rural bureaucrats and self-governing entities independently advance AEE, while market forces and social organizations require enhancement. The study proposes a multi-level governance framework involving rural bureaucrats, villagers' self-governance, market forces, and social organizations to improve AEE. It also highlights the need for differentiated analysis of AEE impacts across crops, grain provinces, and regions. The research employs a fixed effect model and generalized propensity score matching to assess the dynamic effects of digital village construction on AEE, finding that the positive impact increases up to a threshold of 0.8, after which it declines. The study also tests the robustness of findings using a Tobit model and endogeneity tests, confirming the significant positive effect of digital village construction on AEE. Additionally, it examines the regulatory role of rural multi-governance, finding that rural bureaucrats and villagers significantly enhance the positive impact of digital village construction on AEE, while market forces and social organizations have limited effects. The study concludes that digital village construction, supported by multi-level governance, can effectively promote sustainable agricultural development.This study analyzes the role of digital village construction in enhancing agroecological efficiency (AEE) in China, emphasizing its impact on rural governance, including bureaucracies, self-governance bodies, market forces, and social organizations. Using data from 30 provinces (2014–2020), the research explores the dynamics and diversity of multi-level governance in improving AEE. Key findings include a significant positive correlation between digital villages and AEE, though this relationship weakens in an "inverted U" pattern beyond a digital development index of 0.8. Rural bureaucrats and self-governing entities independently advance AEE, while market forces and social organizations require enhancement. The study proposes a multi-level governance framework involving rural bureaucrats, villagers' self-governance, market forces, and social organizations to improve AEE. It also highlights the need for differentiated analysis of AEE impacts across crops, grain provinces, and regions. The research employs a fixed effect model and generalized propensity score matching to assess the dynamic effects of digital village construction on AEE, finding that the positive impact increases up to a threshold of 0.8, after which it declines. The study also tests the robustness of findings using a Tobit model and endogeneity tests, confirming the significant positive effect of digital village construction on AEE. Additionally, it examines the regulatory role of rural multi-governance, finding that rural bureaucrats and villagers significantly enhance the positive impact of digital village construction on AEE, while market forces and social organizations have limited effects. The study concludes that digital village construction, supported by multi-level governance, can effectively promote sustainable agricultural development.