Microchannel systems are emerging as an effective alternative to most of the conventional flow systems. Hence, it is important to understand the transport behaviour in such systems, especially in multiphase flow. Taylor flow regime is generally considered as the most effective regime for heat transfer in two phase flow heat transfer in microchannel systems. In this direction, modelling and experimental studies have been carried out by many researchers and basic understanding of heat transfer behaviour in such systems has been established. The detailed studies for more realistic conditions and effect of various channel geometries are currently being explored. Solid wall and its thickness is an important parameter taken into account while manufacturing such microchannel systems and has great impact on the convective heat transfer behaviour in Taylor flow through microchannels. The same is being studied in this work by carrying out CFD simulations of air-water two phase flow system in a microchannel with the constant wall temperature and constant heat flux conditions. The corresponding results related to variation of wall heat flux, wall temperature and Nusselt number (Nu) along the channel length are presented and discussed in detail. The results indicated that wall thickness causes enhancement in the heat transfer rate and play a significant role in such flow systems. Hence it must be considered for any further related CFD simulation studies as it can help in understanding the more realistic heat transfer behaviour in such systems and hence in designing such system more effectively.