The effects of wettability on multiphase displacement in porous media have been studied extensively in the past, and the contact angle is identified as an important factor influencing the displacement patterns. At the same time, it has been found that effective contact angle can vary drastically in a time-dependent manner on rough surfaces due to Cassie-Wenzel wetting transition. In this study, we develop a theoretical model at the pore scale describing the apparent contact angle on rough interface as a function of time. The theory is then incorporated into the Lattice Boltzmann method for simulation of multiphase displacement in disordered porous media. A dimensionless time ratio, Dy, describing the relative speed of wetting transition and pore invasion is defined. We show that the displacement patterns can be significantly influenced by Dy, where more trapped defending ganglia are observed at large Dy, leading to lower displacement efficiency. We investigate the mobilization of trapped ganglia through identifying different mobilization dynamics during displacement, including translation, coa-lescence, and fragmentation. Agreement is observed between the mobilization statistics and the total pressure gradient across a wide range of Dy. Understanding the effect of wetting transition during multiphase displacement in porous media is of importance for applications such as carbon geosequestration and oil recovery, especially for porous media where solid surface roughness cannot be neglected.