Membrane separation process can simultaneously recover water vapour and waste heat from flue gases, which has great potential for water and energy savings. Composite ceramic nanoporous membrane is one of the emerging technologies showing the good performance of water vapour and waste heat recovery from the flue gas of power plants. However, the flue gas has great property changes along a flue resulting in a dramatic performance change of membrane separation. Current experimental studies couldn’t provide enough experience to explore the performance of membrane modules in a wide range of working conditions and structure configuration. In this paper, a calculation model is established based on thermodynamic mechanisms of membrane separation process to simulate the performance of ceramic membrane modules under different structure configuration and working conditions. Three cases are conducted to analyse the effects of module configuration and parameter selection in a ceramic membrane module. Results show that a ceramic membrane module placed before the desulphurisation tower can recover more heat, while after the desulphurisation tower it can recover more water. There would be an optimal tube diameter and an optimal tube spacing for water recovery under specific working conditions. These results show great adaptability of the calculation model and could guide the system design of membrane separation modules in water vapour and waste heat recovery.