protocols. Among them, qubits with structured noise, especially with biased noise, are one of the most promising platform to achieve fault-tolerance due to the high error thresholds of quantum error correction codes tailored for them. Nevertheless, their quantum operations are challenging and the demonstration of their performance beyond the fault-tolerant threshold remain incomplete. Here, we leverage Schrödinger cat states in a scalable planar superconducting nonlinear oscillator to thoroughly characterize the high-fidelity single-qubit quantum operations with systematic quantum tomography and benchmarking tools, demonstrating the state-of-the-art performance of operations crossing the fault-tolerant threshold of the XZZX surface code. These results thus embody a transformative milestone in the exploration of quantum systems with structured error channels. Notably, our framework is extensible to other types of structured-noise systems, paving the way for systematic characterization and validation of novel quantum platforms with structured noise.