<p>The Agricultural Products Supply Chain (APSC) plays a crucial role in emerging economies such as China and India. Profit distribution, a key driver of stable and sustainable supply chain development, has long been a focus of supply chain research. This paper pioneers the integration of empathy and power structure into the analytical framework, constructing a decision-making model for a three-echelon Agricultural Product E-commerce Supply Chain (APESC) comprising of farmers, agricultural enterprises and e-commerce platforms (e-platforms). To address the limitation of traditional methods that ignore emotional factors in supply chains, a novel “empathy - fair entropy” profit distribution method is proposed. It further explores how empathy and power structure impact APESC profit distribution, leveraging an APESC-tailored empathy utility function, which quantifies abstract empathy into measurable data. The findings demonstrate that consumer empathy toward farmers contributes to higher profits for the entire APESC and all participating entities. However, while moderate empathy from e-platforms boosts profits for farmers, the e-platforms, and the APESCs, it does not benefit agricultural enterprises. The higher power of agricultural enterprises is not conducive to improve the profits of the APESCs. Additionally, the proposed “empathy - fair entropy” method proves more effective in increasing farmers’ profits when agricultural enterprises exhibit low empathy toward farmers. This research expands the theoretical perspective of APESC studies and provides a context-adaptive, operable tool for APESC profit distribution, offering valuable references for supply chain governance in emerging economies.</p>