A method for debugging a logic system design including a target module to be debugged. The method includes receiving a first gate-level netlist associated with the logic system design and a second gate-level netlist associated with the target module that are generated based on a description of the logic system design, obtaining runtime information of an input signal of the target module by running the first gate-level netlist, and obtaining runtime information of the target module by running the second gate-level netlist based on the runtime information of the input signal of the target module.