Against the strategic backdrop of the Fourth Plenary Session of the 20th Central Committee of the Communist Party of China, which emphasizes “accelerating agricultural and rural modernization” and “promoting the deep integration of the real economy and the digital economy,” this paper aims to reveal the underlying mechanisms through which digital transformation reshapes rural income distribution from the perspective of organizational change. The study seeks to provide a theoretical basis for advancing digital village construction and achieving sustained increases in farmers’ income. Grounded in Adaptive Structuration Theory, this paper constructs a comprehensive evaluation system covering digital infrastructure, digital industrialization, and industrial digitalization. Using provincial panel data from China, the study employs multiple econometric methods, including two-way fixed effects models, mediation effect models, panel threshold models, and spatial Durbin models. The findings are as follows: Digital economy promotes the transformation of rural organizational forms from traditional family operations to modern enterprises, platforms, and professional cooperatives through both direct and indirect pathways, albeit with notable regional heterogeneity. The impact of the digital economy on rural residents’ income exhibits a “stepwise increasing” double threshold effect contingent on the level of digital development. Moreover, the digital economy generates significant spatial spillover effects, enhancing local incomes while also benefiting neighboring regions. This study offers important insights for understanding rural organizational transformation and income distribution.