In this work, the Mo microalloying-induced intragranular ferrite and grain refinement are studied through macroscopic experimental research and microstructural simulation. The microstructure and precipitates in high-strength low-alloy steel (DH36 steel) were characterised by an optical microscope and transmission electron microscope to investigate the effect of Mo on fine crystal strengthening and intragranular ferrite induction. It is demonstrated through first-principle calculations that the surface energy of the MoC(100) plane is the lowest and the structural stability is the best, and molecular dynamic simulations confirmed that the phenomena observed in TEM experiments: the α-Fe (100) surface is the optimal orientation surface of the MoC(100) surface. The solidification structure of DH36 steel during the continuous casting process was simulated based on the cellular automaton-finite element (CAFE) model. Based on these observations, solidification structure simulations confirmed the phenomena observed in metallographic experiments. Meanwhile, it is proposed that the grain refinement and microstructure optimisation effect can be controlled by Mo microalloy content, so as to provide important theoretical data for practical shipbuilding steel DH36 production and improvement of the continuous casting quality.