This study addresses the challenge of variable selection in partially linear additive spatial autoregressive models through a novel approach that leverages orthogonal projection based on the QR decomposition technique. This method ensures the validity and compatibility of examining the influence of e-commerce on rural high-quality development while minimizing bias in spatial spillover benefits analysis. By constructing a comprehensive evaluation index system, the research applies a partially linear weighted spatial autoregressive model with orthogonal projection to assess e-commerce’s impact on rural development. Analysis of baseline regression for selected villages, supplemented by heterogeneity tests, threshold effects, and spatial analyses, reveals a significant relationship: a one-unit increase in e-commerce activity corresponds to a 0.0038 unit increase in high-quality rural development. This growth comprises both a direct effect of 0.0011 units and a spillover effect of 0.0027 units, highlighting e-commerce’s pivotal role in promoting rural prosperity and its beneficial spillover to adjacent areas.