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As quantum computing continues to advance, traditional cryptographic methods are increasingly challenged, particularly when it comes to securing critical systems like Supervisory Control and Data Acquisition (SCADA) systems. These systems are essential for monitoring and controlling industrial operations, making their security paramount. A key threat arises from Shor’s algorithm, a powerful quantum computing tool that can compromise current hash functions, leading to significant concerns about data integrity and confidentiality. To tackle these issues, this article introduces a novel Quantum-Resistant Hash Algorithm (QRHA) known as the Modular Hash Learning Algorithm (MHLA). This algorithm is meticulously crafted to withstand potential quantum attacks by incorporating advanced mathematical and algorithmic techniques, enhancing its overall security framework. Our research delves into the effectiveness of MHLA in defending against both traditional and quantum-based threats, with a particular emphasis on its resilience to Shor’s algorithm. The findings from our study demonstrate that MHLA significantly enhances the security of SCADA systems in the context of quantum technology. By ensuring that sensitive data remains protected and confidential, MHLA not only fortifies individual systems but also contributes to the broader efforts of safeguarding industrial and infrastructure control systems against future quantum threats. Our evaluation demonstrates that MHLA improves security by 38% against quantum attack simulations compared to traditional hash functions while maintaining a computational efficiency of O(m · n · k + v + n). The algorithm achieved a 98% success rate in detecting data tampering during integrity testing. These findings underline MHLA’s effectiveness in enhancing SCADA system security amidst evolving quantum technologies. This research represents a crucial step toward developing more secure cryptographic systems that can adapt to the rapidly changing technological landscape, ultimately ensuring the reliability and integrity of critical infrastructure in an era where quantum computing poses a growing risk.