AbstractIn quantum computing, the use of Pauli frames through software traces of classical computers improves computation efficiency. In previous studies, error correction and Pauli operation tracking have been performed simultaneously using integrated Pauli frames in the physical layer. In such a complex processing structure, the number of simultaneous operations processed in the physical layer exponentially increases as the distance of the surface code encoding logical qubit increases. This study proposes a Pauli frame management architecture partitioned into two layers for a lattice surgery‐based surface code and describes its structure and operation rules. To evaluate the effectiveness of our method, we generated a random circuit according to the gate ratios constituting the commonly known quantum circuits and compared the generated circuit with the existing Pauli frame and our method. Simulations show a decrease of about 5% over traditional methods. In the case of experiments that only increase the code distance of the logical qubit, it can be seen that the effect of reducing the physical operation through the logical Pauli frame becomes more important.