In this study, we evaluate mesoscale convective system (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 PyFLEXTRKR algorithm, which defines MCSs based on both cloud top brightness temperature (T_b) and surface precipitation. Results from using only T_b to define MCSs are also discussed to understand the impact of different MCS tracking algorithms on MCS evaluation and provide additional insights into model errors in simulating MCSs. Our results show that EAMv2 simulated MCS precipitation is largely underestimated in tropical and extratropical regions. This is mainly attributed to the underestimated MCS genesis and underestimated precipitation intensity in EAMv2. Comparing the two MCS tracking methods, simulated MCS precipitation is increased if MCSs are defined with only cloud top T_b. The T_b-based MCS tracking method, however, includes cloud systems with very weak precipitation. This illustrates the model issues in simulating heavy precipitation even though the convective cloud shield is overall well simulated from the moist convective processes. Furthermore, sensitivity experiments are performed to examine the impact of new cloud and convection parameterizations developed for EAMv3 on simulated MCSs. The new physics parameterizations help increase the relative contribution of convective precipitation to total precipitation in the tropics, but the simulated MCS properties are not significantly improved. This suggests that simulating MCSs still remain a challenge for the next version of E3SM.