MicroRNA (miRNA)-124 inhibitor may enhance cerebral blood vessel formation in lacunar cerebral infarction (LCI) and mesoporous silica nanoparticles are highlighted as a drug carrier which improves patients' outcome. This study explored the impact of miR-124 and its promising targeted gene P2Y12 encapsulated by mesoporous silica nanoparticles (MSNs) on progression of LCI, and its interaction between SCF/c-kit signaling pathway. After establishment of animal models, the animals were divided into 6 groups, namely: model group, blank group, empty carrier group, carrier + miR-124 inhibitor group, SCF/c-kit inhibitor group, and P2Y12 agonist group. Western blot analysis and microscope determined the expression level of miR-124 in the rat brain tissue slices. MVD, SCF and c-kit P2Y12 protein expression levels were detected and their targeting relationship was verified. miR-124 was poorly expressed in the cells of rats with LCI upon injection of MSNs carrying miR-124-inhibitor. The LCI model group had the highest number of VEGF-positive. Compared with the model group, the number in the carrier + miR-124 inhibitor group was lowest. Moreover, treatment with SCF/c-kit inhibitor and P2Y12 agonist also obtained reduction in the number of VEGF-positive cells with less prominent effect (P < 0.05). With elevation of MVD in the LCI rats, injection of P2Y12 agonist or SCF/c-kit inhibitor significantly decreased the amount of MVD, while miR-124 inhibitor-loaded MSNs better reduced the MVD level. Besides, the LCI rats exhibited up-regulated level of P2Y12 protein. Injection of P2Y12 agonist or SCF/c-kit inhibitor dramatically decreased the level of P2Y12, where the level was still higher than that of carrier + miR-124 inhibitor group. Moreover, administration of miR-124 inhibitor-loaded MSNs resulted in increased SCF and c-kit protein level, and SCF/c-kit inhibitor group and P2Y12 agonist group also had increased SCF and c-kit protein level, compared to the model group. Mechanistically, the miR-124 was indicated to target P2Y12 with stronger fluorescence intensity in mutant plasmid (P < 0.05). MSN-encapsulated miR-124 inhibitor increased the expression of SCF/c-kit protein by targeting P2Y12, thereby enhancing regeneration of cerebral blood vessels in LCI.