Disclosed is a quantum computing system including a first quantum chip including first physical qubits, a second quantum chip including second physical qubits, and a management device. The management device includes a physical qubit layer that manages physical qubit mapping including information about physical channels between first and second physical qubits, an abstraction qubit layer that manages abstraction qubit mapping including information about abstraction qubits and abstraction channels between the abstraction qubits based on the physical qubit mapping, a logical qubit layer that divides the abstraction qubits into logical qubits and to manage logical qubit mapping including information about logical channels between the logical qubits, based on the abstraction qubit mapping, and an application qubit layer that allocates at least one logical qubit corresponding to a qubit request received from a quantum application program based on the logical qubit mapping.