Shrinkage-induced cracking significantly impacts the durability of mass concrete structures. Quantitatively evaluating drying shrinkage of concrete proves challenging due to the time-consuming experiments and overlooked microstructure changes during the hydration process. To address this concern, this study initially characterized the long-term hydration products and microstructure of low-heat Portland cement (LHPC) through microstructural experiments. Subsequently, a novel high-resolution mesoscale framework is developed to investigate the drying shrinkage with hydration kinetics. High-resolution models consist of realistic-shaped aggregates are validated by the aggregate morphology and gradation parameters of core sample from mass concrete. Concurrently, the quantitative effects of internal and external factors on LHPC drying shrinkage are explored. Results indicated that LHPC possesses a denser microstructure, lower porosity, higher carbonation resistance, and 20% lower drying shrinkage compared to moderate-heat Portland cement, suggesting promising applications. Furthermore, experimental and computational findings suggested that increasing aggregate volume, controlling aggregate morphology, and adjusting curing time and humidity could be employed to reduce and manage drying shrinkage, ensuring concrete structure durability.