Abstract
Quantum Error Correction (QEC) codes form the foundation of Fault-Tolerant Quantum Computing (FTQC) and predominantly use the Clifford+T gate set. Recently, Clifford operations have become the key performance bottleneck in implementing QEC. While state-of-the-art approaches like Pauli-Based Compilation (PBC) reduce Clifford overhead by transforming Clifford gates into Pauli measurements, they do so at the cost of gate-level parallelism, inflating circuit depth and execution times. To overcome these limitations, we introduce TACO, a Transpiler-Architecture Co-design framework that tackles the Clifford bottleneck through circuit and architectural optimization. TACO uses FTQC insights to guide hardware-aware Clifford gate elimination and circuit restructuring, and leverages the resulting optimized circuits to refine architectural design. TACO applies FTQC-specific transformations to aggressively reduce Clifford overhead from rotation synthesis and Toffoli decompositions, while preserving gate-level parallelism. The resulting architecture is optimized for the locality and data-movement patterns of these circuits, enabling high-throughput, resource-efficient execution. Our evaluation across diverse benchmarks shows that TACO achieves up to 21.9x (mean 4.4x) reduction in execution time compared to the state-of-the-art baseline.