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Under China’s rural revitalization and agricultural modernization strategies, digital village construction overcomes resource limits to drive transformation. Using 2013–2022 provincial panel data and a case study of Lin’an, Hangzhou, this study reveals how digital villages boost high-quality agriculture. The empirical results show they significantly enhance agricultural total factor productivity via three paths: IoT-driven precision production, blockchain-enabled green value addition, and e-commerce direct sales demonstrate more pronounced effectiveness in major grain-producing regions and those characterized by balanced production and sales. Simultaneously, this study employs the instrumental variable (TI) approach to address endogeneity from reverse causality and omitted variables. Mechanism testing reveals agricultural technological innovation exerts a significant 77.5% mediating effect. Finally, digital rural construction exhibits a non-linear threshold (0.3082); surpassing it triggers a gradual slowdown in growth with decreasing marginal returns. The Lin’an case validates the empirical results while revealing structural barriers, including industrial chain penetration gaps, data silos, and factor supply constraints, leading to the formulation of targeted optimization strategies. The practical contribution of this study is the proposal of a “data-value-technology” closed loop: public brands like “Tianmu Mountain Treasures” channel premiums into R&D funds, creating a self-sustaining mechanism. The findings indicate that digital villages drive high-quality agriculture primarily through direct effects, powered by full-chain tech coordination, institutional reform, and inclusive factor supply. Finally, this study proposes a coordinated governance framework encompassing “technical synergy, institutional innovation, and factor optimization,” providing theoretical support and strategic references for optimizing the pathways of regional agricultural digital transformation.