This work aims to develop and techno-economically analyze a novel coal-based polygeneration process of Molten Carbonate Fuel Cell (MCFC) and methane synthesis with a waste heat recovery system. In this process, the unshifted syngas without entering Rectisol is directly mixed with a part of H2-rich syngas to reduce the energy consumption of Rectisol and flexibly adjust the H/C ratio. An extended Duran-Grossmann (D-G) model for waste heat recovery steam cycle optimization is proposed by conducting Heat Integration among the whole process. According to techno-economic analysis, the annual capital cost of the proposed system is 50,006,000 $, the overall exergy efficiency is 56.3 %. Compared with the base plant, the MCFC with power generation of 16.98 MW is applied instead of the Rankine cycle (RC), which results in a 14 % increase in the efficiency of the power generation system. The major contributions derived from this work are of significant aid in highlighting strong potentials for overall performance enhancement via polygeneration optimization.