Objectives: Engineering spheroids to create three-dimensional (3D) cell cultures has gained increasing attention in recent years due to their potential advantages over traditional two-dimensional (2D) tissue culture methods. Stem cells derived from human exfoliated deciduous teeth (SHEDs) demonstrate significant potential for pulpal regeneration applications. Nevertheless, the feasibility of microsphere formation of SHEDs and its impact on pulpal regeneration remain unclear. Methods: In this study, SHEDs were isolated, identified, and cultured in ultra-low attachment six-well plates to produce SHED microspheres. The biological properties of SHED microspheres were compared to those of traditional 2D culture using live-dead staining, Alizarin red staining, Oil-red O staining, scratch experiments, Immunofluorescence, Transmission electron microscopy scan, Western blotting, RNA sequencing, and a nude mice subcutaneous transplantation model. Results: We found SHED cells can form microspheres with a dense internal structure. SHED microspheres exhibited notable advantages over SHED cells in terms of biological properties, maintaining cell activity and enhancing cell differentiation, migration, and stemness in vitro. RNA-seq revealed that the SHED microspheres potentially influenced cell development, regulation of neurogenesis, skeletal system development, tissue morphogenesis singling pathway. In vivo, SHED microspheres promoted the generation of pulp tissue in dental pulp compared to traditional 2D culture. Conclusions: Microsphereization of SHED through 3D cell culture enhances its pulp regeneration capacity, presenting a novel strategy for dental pulp regeneration and the clinical treatment of dental pulp diseases.