This paper proposes a polygeneration system based on a multi-input chemical looping combustion system, which generates methanol and electricity, through the use of natural gas and coal. In this system, the chemical looping hydrogen (CLH) production system and the coal-based methanol production system are integrated. A high quality fuel, natural gas, is used to improve the conversion ratio of coal. The Gibbs energy of the two kinds of fuels is fully used. Benefitting from the chemical looping process, 27% CO2 can be captured without energy penalty. With the same outputs of methanol and electricity, the energy savings ratio of the new system is about 12%. Based on the exergy analyses, it is disclosed that the integration of synthetic utilization of natural gas and coal plays a significant role in reducing the exergy destruction of the new system. The promising results obtained in this paper may lead to a clean coal technology that will utilize natural gas and coal more efficiently and economically.