Advanced efficient energy conversion technology using clean alternative fuel contributes to the alleviation of the energy crisis and environmental deterioration. In this situation, a novel methanol utilization technology for power generation based on hybrid fuel cell system is proposed in this work. The hybrid system consists of a solid oxide fuel cell (SOFC), a gas processing unit (GP) and a proton exchange membrane fuel cell (PEMFC). Thermodynamic analysis of the system shows that the energy conversion efficiency and exergy efficiency are both higher than the previously reported standalone or hybrid energy systems using methanol as fuel, which are 66.2% and 54.2% respectively. Besides, no recirculation ratio of anode off-gas and moderate fuel utilization of about 0.5 are suggested for the SOFC component to balance the power distribution and improve the efficiency. Afterwards, this hybrid fuel cell system is also investigated from thermo-economic and techno-economic perspectives. Take Northwest China as a case, the 1 MWe methanol-fed power plant has a specific electric energy cost of 0.5594 CNY/kWh, much lower than the methanol steam reforming-PEMFC power plant (2.4 CNY/kWh). At the same time, the sensitivity analyses reveal that the cost of the hybrid power system is not sensitive to the market price fluctuation. With financial subsidies for existing renewable power plants, the payback period can be shortened to 1.4 year and the annual return on investment is about 3.58%. These results reveal that this two-stage fuel cell hybrid system is a kind of efficient and economically methanol to power conversion technology, especially for small power scale.