Energy efficiency is a growing priority in architecture, engineering, and construction (AEC) due to the pressing challenges of climate change and rising electricity costs. These challenges further emphasize the need for innovative low-energy solutions and certifications to guide the design of energy-efficient buildings in sustainable smart cities. Existing certifications primarily emphasize energy consumption but often overlook critical aspects like occupant comfort and satisfaction, contributing to a “building performance gap”—the difference between expected and actual building performance, largely influenced by user behavior. This study aims to address these limitations by developing a Zero-energy Building (ZEB) rating framework tailored for sustainable smart cities by integrating digital twin technology. Focusing on the design and operation of energy-efficient, climate-resilient buildings aligned with the principles of sustainable smart cities, this study illustrates how digital twins can be integrated into sustainable smart city management, promoting coordinated and holistic urban solutions. This integration allows city planners to simulate different scenarios, optimize resource allocation, and ultimately create urban environments that are more efficient and resilient. The study demonstrates that digital twins serve as an effective tool for constructing a ZEB rating system by enabling dynamic and real-time assessments. By identifying and integrating key parameters—such as energy consumption patterns, occupant comfort metrics, and system efficiency benchmarks—into the design framework, digital twins enable city planners and developers to bridge the gap between theoretical models and actual building performance. This approach ensures that the rating system is comprehensive and practically applicable across various urban contexts, facilitating more accurate assessments of building efficiency and sustainability in real-world environments. This study fosters the development of sustainable, climate-resilient smart cities that are well-prepared to meet future environmental challenges. The integration of digital twins enables urban stakeholders to make informed decisions, ensuring that buildings are optimized for both energy efficiency and occupant well-being, thus advancing the goals of sustainable urban development.