Supernumerary tooth-derived pulp stem cells (SNTSCs) hold promise for endodontic regeneration, yet little is known about the similarities and diversities of SNTSCs relative to other dental-derived mesenchymal stem cells. Herein, we compare the biological characteristics of SNTSCs with dental pulp stem cells (DPSCs) and stem cells from human exfoliated deciduous teeth (SHED). Cell proliferation, migration, and odontogenic differentiation potential, as well as viability and aging-related phenotype after long-term storage, were evaluated. Additionally, gene expressions during induced odontogenic differentiation were profiled by transcriptome sequencing. Our findings indicated that the SNTSCs outperformed the DPSCs but were inferior to the SHED in cell proliferation. The SNTSCs exhibited comparable migratory capacity to the SHED and surpassed the DPSCs. Of particular interest, the odontogenic differentiation potential followed the pattern of SHED > SNTSCs > DPSCs. After two years of storage, the SNTSCs showed weakness in resistance to apoptosis induced by lipopolysaccharide, whereas difference between the SNTSCs and SHED in stemness and senescence was not obvious. Transcriptome analysis revealed that upregulated genes in the SNTSCs were particularly enriched in inflammatory signaling pathways compared to both the DPSCs and SHED. Collectively, SNTSCs share many satisfactory features in proliferation and differentiation with SHED, which may serve as a promising alternative cell source for endodontic regeneration.