Fuel reforming strategy is a promising new technology to improve the combustion performance of the fuel in engines. The flexible cylinder engine (FCE) mode is a new concept, by optimizing the property of the fuel via low-temperature reforming in a flexible cylinder. The FCE mode consists of three processes, i.e., reforming, cooling, and working processes. In this work, the primary reference fuel of PRF90 was adopted to demonstrate the FCE mode in a homogeneous charge compression ignition engine, mainly comparing the effects of three typical cooling strategies, i.e., linear, natural, and delayed cooling, on the reformed products and, hence, the combustion performance of the fuel in the normal cylinders theoretically. The simulations were performed using the CHEMKIN package. The ignition delay time was decreased dramatically under the FCE mode with the three cooling strategies. The potential in decreasing the ignition delay time is in the order of linear cooling > normal cooling > delayed cooling. The laminar flame speed was increased slightly under the FCE mode. The delayed cooling strategy performed best in reducing the harmful emissions of carbon monoxide and unburned hydrocarbon among the three cooling strategies. From the point view of energy efficiency and emissions, the delayed cooling strategy should be adopted in practical engines under FCE mode.