Agriculture is a cross-cutting sector that produces 26.5% of GDP and employs 56% of the workforce in Cambodia. However, the unsustainable situation of traditional agriculture system contributes to low income capability and farmers are likely to remain below the poverty line. Therefore, we put forward a comprehensive e-commerce application model, a creative leverage of ICT-driven solution that could offer farmers up-to-date information, customized knowledge, input and services to enhance productivity and farm gate realization. This application model is tailored from e-commerce framework for rural agriculture sector which focuses on two main directions; of reshaping agriculture production and restructuring market orientation. There are six dynamic components in this application model mainly the e-commerce gateway, supply chain management, real-time info and search engine, multimedia and social network, knowledge based information system, and finally infrastructure and internet connection. This model will then become the basis for n-tier e-commerce application system requirements; from user-centered design principles, web development approach, client terminal and gateways, and infrastructure for internet connectivity. And lastly is the specific participatory approach for e-commerce application system that allows decision making among farmers towards rural development and empowerment.