Rhombohedron-like and fusiform calcium carbonate nanoparticles were fabricated using a new method. Their geometry was controlled by varying the mixing speed and ratio of ethanol versus water in reaction system. The calcium carbonate nanoparticles (CCNPs) have slight effect on viability of human bone-marrow mesenchymal stem cells (hBMSCs) with dose-dependent and shape-dependent, but they can significantly promote osteogenic differentiation of hBMSCs in vitro by 10–37％ increase of alkaline phosphatase (ALP) activity, 9–36％ growth of collagen secretion and 1.13–1.83 folds upregulation of osteogenesis-related genes, even at lower dose ranges (5–20 μg/ml). The efficacity of promoting osteogenesis depends on the shape and dose of CCNPs. Furthermore, adipogenesis was inhibited by less accumulation of lipid droplets, lower triglyceride (TG) secretion and downregulation of adipogenesis-related genes. These findings improve the understanding of effects CCNPs on hBMSCs fate towards osteoblasts or adipocytes and have meaningful impact for combining use of CCNPs and hBMSCs in tissue engineering and regenerative medicine fields.