Reducing the energy penalty for CO2 Capture and Storage (CCS) is a challenge. Most of previous studies for CCS have been focused on power generation system. When CCS is included in the polygeneration system, a new methodology that jointly considering CCS and liquid fuel production should be introduced. In this paper, we proposed a new approach integrating CCS into a coal-based polygeneration system for power generation and methanol production: the syngas produced from the coal gasifier, without adjusting the composition (CO/H2 ratio) by shift reaction, is used to synthesis methanol directly. Moreover, the partial-recycle scheme, in which a part of unreacted gas is recycled back to the synthesis reactor, is adopted in the synthesis unit. Another part of unreacted gas is treated to remove CO2, and then is used as clean fuel for the power generation subsystem. Compared to the conventional CCS approaches adopted by the power generation systems, the new approach is mainly characterized by two features: firstly, the combination of the removal of the composition adjustment process and a partial-recycle scheme can not only reduces the energy consumption for methanol production, but also obtains a high concentration of COX (CO and CO2) in the unreacted gas; secondly, the CO2 is captured from the unreacted gas, instead of from syngas generated by the gasifier. Due to increment of COX concentration, the new approach can reduce the energy consumption for CO2 capture compared to conventional pre-combustion CO2 capture. In the conventional coal based IGCC systems, the thermal efficiency is around 34-36% for a case with CO2 capture and around 44% for a case without CO2 capture. However, with the innovative approach integrating CCS, the polygeneration system in this paper can achieve the equivalent thermal efficiency as high as 47% when 72% of CO2 is recovered, which provides a significant improvement for CO2 capture. It’s clearly that the new approach can increase the thermal efficiency, instead of incurring an energy penalty for CO2 capture. The results achieved in this study have provided a new methodology integrating CO2 capture into the polygeneration system, which reveals the different characteristics compared to power-generation system that has been overlooked by the previous studies.