Osteogenic differentiation of dental pulp stem cells (DPSCs) is considered as a promising strategy in posterior maxilla tooth implantation. Information on the function and mechanisms of long non-coding RNAs (lncRNAs) in osteogenic differentiation of DPSCs is growing, however, the mechanism of LINC00968 and miR-3658 in regulating osteogenic differentiation of DPSCs still needs to be explored. In this study, the LINC00968 and miR-3658 expression level was upregulated and downregulated in DPSCs and peri-implantitis DPSCs (pDPSCs) treated with bone morphogenic protein (BMP)2, respectively. Moreover, the effects of LINC00968 and miR-3658 on BMP2-induced osteogenic differentiation of DPSCs in vitro using Alizarin Red S staining, alkaline phosphatase (ALP) activity, quantitative real time PCR and Western blot assays showed that overexpression of LINC00968 significantly promoted mineralized bone matrix, alkaline phosphatase (ALP), runt-related transcription factor 2 (RUNX2), and osterix (OSX) expression levels for osteogenic differentiation of DPSCs and pDPSCs; and overexpression of miR-3658 showed an opposite result that inhibited osteogenic differentiation of DPSCs and pDPSCs. Luciferase reporter assay showed that luciferase activities of LINC00968-WT reporter and RUNX2-WT reporter were strongly suppressed by miR-3658 overexpression. In addition, the miR-3658 upregulation interfered ectopic bone formation in vivo stimulated by LINC00968. In general, we had identified a novel molecular pathway involving LINC00968/miR-3658/RUNX2 during DPSCs and pDPSCs differentiation into osteoblasts, which might facilitate bone anabolism.