In the agricultural sector where the fossil fuels are primary energy resources, the current global energy crisis together with the dissemination of smart farming has led to the new phase of energy pattern in which the electricity demand is growing faster particularly. Therefore, the fuel cell combined heat and power system, coupling the environmentally friendly fuel cell to biomass treatment and feeding, can be regarded as the most effective energy system in agriculture. In this mini-review, we discuss the R&D trend of the fuel cell combined heat and power system aimed at utilizing agricultural by-products as fuels and highlight the issues in terms of the process configuration and interconnection of individual processes.