Contractive chemical shrinkage of hydrating cement paste leads to microcracking due to aggregate restraint. This paper explores the role of sealed hydration kinetics on microcrack formation in cement mortars by means of 4D μ-CT technique with the resolution of 2.2 µm. The test used three binders; a finely-ground ordinary Portland cement (OPC) with Blaine fineness of 391 m2/kg, a coarsely-ground OPC from the same clinker with the fineness of 273 m2/kg, and an alkali-activated H-cement. The results show that microcracks exhibit characteristic width 5–15 µm and increase their occurrence between monitored time 2 and 4 weeks. The coarsely-ground OPC and H-cement exhibited comparable number of microcracks at 2 and 4 weeks while the finely-ground OPC exhibited more than twice the number of microcracks. Mesomechanical simulation performed on 2D images proves that high shrinkage rate induces more microcracks due to smaller stress relaxation. The paper demonstrated, both experimentally and numerically, that higher strength gain by accelerated hydration leads to higher internal microcracking, generally impairing durability by microcracks coalescence into visible cracks. In this regard, durable concrete shall be based on slow hydration or should incorporate alkali-activation processes to reduce microcracks.