The regeneration of large-scale bone loss due to accidents, trauma, diseases, or tumor resection is still a critical clinical challenge. With the development of additive manufacturing technology and advanced biomaterials, 3D-printed biocompatible synthetic polymer scaffolds have been widely studied for their key roles in supporting bone tissue regeneration. Scaffold aims to provide mechanical properties that match the host bone as well as biological activities that can effectively promote cell proliferation and differentiation, ultimately facilitating bone tissue regeneration. Due to its unique biocompatibility and biodegradability, polycaprolactone (PCL) becomes one of the dominant synthetic polymeric materials considered for scaffold fabrication. However, using PCL alone presents insufficient mechanical properties; thus, different functional fillers have been added to modulate both the mechanical and biological performance of fabricated scaffolds. Among all functional fillers, carbon nanomaterials, particularly graphene (G), have shown an emerging trend. Graphene quantum dots (GQD), a member of the graphene family, are regarded as an ideal next-generation functional filler for scaffold fabrication. It presents high solubility in water, controllable dose-dependent cytotoxicity similar to that of G, and unique biological properties benefiting from smaller sizes. Current research using GQD for tissue engineering applications is limited, and the systemic comparison between G and GQD at different concentrations is also missing. This study, for the first time, evaluates and compares the impact of incorporating G and GQD into PCL bone tissue engineering scaffolds from surface, thermal, mechanical, and biological perspectives. Results suggested that the addition of both materials under 5 wt % significantly improved both the mechanical and biological performance of PCL scaffolds. Under 3 wt %, PCL/GQD scaffolds presented better compressive strength while maintaining the same level of biological performance compared with PCL/G scaffolds, revealing the strong potential for future in vivo studies and bone tissue regeneration applications.