For bone regenerative engineering, it is a promising method to form skeletal tissues differentiating from human bone morrow mesenchyme stem cells (hBMSCs). However, it is still a critical challenge to efficiently control ostogenesis and clearly reveal the influence factor. To this end, the fluorescent gold nanodots (Au NDs) with highly negative charges as osteogenic induction reagent are successfully synthesized, which display better than commercial osteogenic induction medium through the investigations of ALP activity (2.5 folds) and cytoskeleton staining (1.5 folds). Two kinds of oligopeptides with different bio-structures (cysteine, Cys and glutathione, GSH) are selected for providing surficial charges on Au NDs. It is revealed that Au-Cys with more negative charges (-51 mV) play better role than Au-GSH (-19 mV) in osteogenic differentiation, when both of them have same size (～2 nm), sphere shape and show similar cell uptake amount. To explore deeply, osteogenesis related signaling pathways are monitored, revealing that the enhancement of osteogenic differentiation was through autophagy signaling pathway triggered by Au-Cys. And the promotion of highly negative charges in osteogenic differentiation was further proved via sliver nanodots (Ag NDs, Ag-Cys and Ag-GSH) and carbon nanodots (CDs, Cys-CDs and GSH-CDs). This work indicates part of insights during hBMSCs differentiation and provides a novel strategy in osteogenic differentiation process.