As an important distribution channel for agricultural products, rural e-commerce exerts significant influence on agricultural production. Based on a survey of 604 Fuji apple farmers in Shanxi Province, this study empirically examines the effect of participation in e-commerce on farmers’ fertilizer application behavior, from the perspectives of increasing the price premium for green products and reducing the cost of green production. To address potential endogeneity, this study proposes an innovative instrumental variable—the distance to the birthplace of Guan Gong—to alleviate the bias caused by unobserved factors. The findings reveal that participation in e-commerce reduces farmers’ fertilizer application intensity. This effect is more evident among farmers with larger land operation scales, larger contiguous plots, and a higher degree of production specialization. Furthermore, the analysis shows that farmers with higher levels of digital literacy and green production literacy benefit more from e-commerce participation in terms of reducing fertilizer input intensity. Overall, this study confirms that participation in e-commerce enables green agricultural production while imposing higher demands on land operation scale, production specialization, and farmer literacy, offering new directions for promoting sustainable and environmentally friendly agricultural practices.