Biogas is an important renewable energy in underdeveloped mountainous areas. Through questionnaire surveys of biogas users in the underdeveloped mountainous areas in Fujian Province, six typical modes of the biogas operation system were determined, namely, the biogas welfare-supply mode, commodity-producer mode, characteristic-planting mode, working and farming combination mode, traditional farming and breeding mode, and professional-breeding mode. Among these, the first two belong to the supply type, whereas the later four are the self-sufficient type. In this study, based on the emergy theory, we used the emergy indexes analysis system. The six typical modes were first studied to determine differences in their input and output composition, system performance, and system sustainable development ability. Next, by calculating the emission reduction of greenhouse gases, the emission reduction benefits of the six modes were estimated. Finally, differences in the financial investment in government subsidies for the six typical modes were determined by cost-benefit analysis. The study results showed that (1) regarding emergy input-output, supply-type biogas invested large amounts of purchased non-renewable emergy and realized high efficiency and high yields for production. Conversely, self-sufficient biogas was characterized by a high utilization rate of natural resources and low environmental load rates, with a large investment of purchased renewable emergy. In terms of system performance, the high net emergy yield ratio and emergy exchange ratio for supply-type biogas was better than that of the self-sufficient type because the later exhibited insufficient output. With the highest net emergy yield ratio and emergy exchange ratio, the commodity-producer mode had the best system performance among the six modes. (2) Regarding ecological benefits, modes including welfare mode, commodity-producer mode, and professional livestock-raising mode were prominent in the reduction of emission effects of greenhouse gases because their main income was from breeding. The modes including characteristic-planting mode, working and farming-combination mode, and traditional farming and breeding mode were not obvious in the reduction of the emission of greenhouse gases because their main development was planting. (3) From the perspective of government subsidies, the financial investment feasibility of the six modes was demonstrated at two angles, which were the farmer household financial angle and social economic angle. For the farmer household financial angle, welfare mode, commodity-producer mode, and professional-breeding mode could not satisfy the standard of farmer household financial investment. However, because of high ecological benefits from emission reduction of greenhouse gases, they conformed to the financial feasibility standard of the social economic point of view. On the other hand, the characteristic-planting mode and working and farming combination mode could not meet the financial feasibility standard of the social economic point of view, but satisfied the farmer household financial standard. Only traditional farming and breeding mode fully met the needs of social economic perspectives and the perspective of the farmer household financial standard. Based on the above research results, according to the breeding scale developmental trend and the present situation regarding energy utilizing in the underdeveloped mountainous area, some suggestions were proposed for choosing the appropriate development mode of biogas plant construction in the study area.