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• Hybrid bottom-up model to integrate geo-referenced and synthetic stock models. • Demonstrate multi-scale and long-term transitional workflow for commercial building stock. • Identify drivers and determinants of energy usage in the commercial building stock. • 32% cumulative performance gap if concurrent consideration of physical and technical factors is disregarded. • Introducing the unit block concept to determine minimum viable requirements. For energy modelling of commercial building stock (CBS), several methodologies were developed focusing on technology alternatives and retrofits for climate change mitigation, but they often have limitations to involve a differentiated description of practices and policies across a range of scales and sectors. This paper presents a novel hybrid model by integrating spatial and synthetic modelling approaches to facilitate the concurrent consideration of multiple building-oriented elements. The model is further implemented on Japanese building stock to demonstrate multi-scale and long-term framework for energy modelling of CBS. The results indicate the following findings: the scale choice introduces significant variability in energy consumption estimation with a relative error of 10–17% mainly depending on building geometry and plug loads; the long-term model exhibits a higher scale-bounded uncertainty in terms of energy saving potential that varies by 2–3 times when a non-representative scale is applied; disregarding physical and technical factors results in a cumulative performance gap of up to 32%; and the accuracy and extent of the model across the stock are more sensitive to technical factors, such as building system stock dynamics and the heterogeneity of HVAC systems, than physical factors. The model provides a multi-tier framework using spatial intelligence building stock approach to develop long-term energy efficiency monitoring strategies for CBS. [ABSTRACT FROM AUTHOR]