A system and method for netlist clock domain crossing verification leverages RTL clock domain crossing (CDC) verification data and results. The netlist clock domain crossing verification system (NCDC) migrates RTL-level constraints and waivers to the netlist design so that the user does not have to re-enter them. The NCDC checks the netlist and generates a report that compares RTL-level CDC checking results to the netlist-level CDC checking results to make it easy to see new issues. The NCDC receives and stores netlist corrections from user input or automatically corrects certain CDC violations, in the netlist.