Quantum Key Distribution (QKD) provides information-theoretic security, yet its practical deployment is strongly constrained by channel noise, timing uncertainty, and vulnerability to synchronization disturbances, particularly in noisy intermediate-scale quantum (NISQ) systems. This paper proposes a synchronization-aware QKD protocol in which timing estimation and key generation are explicitly integrated at the protocol level. The scheme embeds frame-level clock offset estimation, time-domain detection filtering, and adaptive coincidence-window control directly into the QKD workflow, allowing synchronization quality to directly govern key acceptance. The protocol operates on discrete, time-tagged single-photon detection events and does not rely on continuous pulse assumptions. Timing uncertainty arising from detector jitter and bounded adversarial delay is reflected in the synchronization acceptance probability and contributes explicitly to the quantum bit error rate (QBER). A hybrid simulation framework combining NetSquid-based quantum-layer modeling with event-driven classical control is used to evaluate protocol performance under realistic detector and channel parameters. Simulation results demonstrate that adaptive detection-window control effectively mitigates performance degradation due to timing jitter and bounded delay attacks, maintaining positive finite-key secure key rates and fidelity above (97%) under realistic operating conditions. Comparative evaluation against BB84, E91, Twin-Field QKD, and High-Dimensional QKD indicates improved tolerance to timing uncertainty and adversarial delay without modifying the underlying QKD primitives. These results highlight the importance of synchronization-aware design for robust QKD operation and support the feasibility of the proposed approach in practical quantum communication networks.
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