Background/purpose Dental pulp stem cells (DPSCs) are candidate seed cells for bone tissue engineering, but the molecular regulation of osteogenic differentiation in DPSCs is not fully understood. Long non-coding RNAs (lncRNAs) are important regulators of gene expression, and whether they play roles in osteogenic differentiation of DPSCs requires more study. Materials and methods DPSCs were isolated and cultured. The mRNA and lncRNA expression profiles were compared through microarray assay between osteo-differentiated DPSCs and non-differentiated DPSCs. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, Gene ontology (GO) analyses, and the mRNA-lncRNA co-expression analyses were performed for functional annotation of differentially expressed RNAs. Small interfering RNA (siRNA) was used to interfere the expression of lncRNA ENST00000533992 (also named smooth muscle-induced lncRNA or SMILR), a candidate regulator, then the osteogenic differentiation potential of DPSCs was analyzed. Results DPSCs were isolated and cultured successfully. The expression of 273 mRNAs and 184 lncRNAs changed significantly in DPSCs after osteogenic induction. KEGG analyses and GO analyses showed that the differentially expressed RNAs were enriched in several pathways and biological processes. The mRNA-lncRNA co-expression network was constructed to reveal the potential relationships between mRNAs and lncRNAs. The osteogenic differentiation potential of DPSCs decreased when SMILR was interfered. Conclusion The present study provides clues for seeking for lncRNAs that participate in the regulation of osteogenic differentiation in DPSCs. LncRNA SMILR could play a role in regulating osteogenic differentiation of DPSCs.