A carbon chain analysis is applied to assess a complex energy conversion system with CO2 capture and storage (CCS). A coal integrated gasification combined cycle, with CCS, which co-produces electricity and liquid fuels (IGCC–LF–CCS) is taken as a case study. A process simulation method is used to estimate the technological data, and balance the heat and electricity for the whole system. Carbon and energy flows are calculated to evaluate the mass conversion efficiency and the energy efficiency. The results show that in the case in which one third of the coal is allotted to synthesize liquid fuels, globally 60% carbon is captured for storage, 19% transferred to liquid fuels, 19% emitted to the atmosphere, while the remaining carbon is discharged as waste. For the energy flow, 28.1% of total higher heating value of coal is converted into the liquid fuels. The net electricity efficiency is 20.7% accounting for the power demands by air separation, CO2 capture and compression. Three scenarios with different ratio of resource to produce electricity and liquid fuels with or without CCS have been studied. This work will provide useful information for the coal utilization with CCS in a carbon-constrained world. Copyright © 2012 Elsevier B.V. All rights reserved.