Mesoscale convective systems (MCSs) play an important role in modulating the global hydrological cycle, general circulation, and radiative energy budget. In this study, we evaluate MCS simulations in the second version of U.S. Department of Energy (DOE) Energy Exascale Earth System Model (E3SMv2). E3SMv2 atmosphere model (EAMv2) is run at the uniform 0.25° horizontal resolution. We track MCSs consistently in the model and observations using the PyFLEXTRKR algorithm, which defines MCS based on both cloud-top brightness temperature (Tb) and surface precipitation. Results from using Tb only to define MCS, commonly used in previous studies, are also discussed. Furthermore, sensitivity experiments are performed to examine the impact of new cloud and convection parameterizations developed for EAMv3 on simulated MCSs. Our results show that EAMv2 simulated MCS precipitation is largely underestimated in the tropics and contiguous United States. This is mainly attributed to the underestimated precipitation intensity in EAMv2. In contrast, the simulated MCS frequency becomes more comparable to observations if MCSs are defined only based on cloud-top Tb. The Tb-based MCS tracking method, however, includes many cloud systems with very weak precipitation which conflicts with the MCS definition. This result illustrates the importance of accounting for precipitation in evaluating simulated MCSs. We also find that the new physics parameterizations help increase the relative contribution of convective precipitation to total precipitation in the tropics, but the simulated MCS properties are overall not significantly improved. This suggests that simulating MCSs will remain a challenge for the next version of E3SM.