Disclosed herein are a quantum simulation apparatus and method using logical qubit synthesis. The quantum simulation apparatus is configured to generate a new virtual quantum device configured using magic qubits by dividing each logical qubit into multiple areas, extract logical qubit information from a target virtual quantum device that is a target of a logical Controlled NOT (CNOT) operation, synthesize the extracted logical qubit information into the new virtual quantum device, perform a logical CNOT operation in the synthesized virtual quantum device, extract logical qubit information from a result of the logical CNOT operation in the synthesized virtual quantum device, and synthesize the logical qubit information extracted from the result of the logical CNOT operation into the target virtual quantum device.