Scaffold architecture is a key determinant of cell behavior and tissue regeneration in bone tissue engineering, yet the influence of pore size under dynamic culture conditions remains incompletely understood. This study aimed to evaluate the effects of scaffold pore size on osteogenic differentiation of porcine bone marrow-derived mesenchymal stem cells (pBMSCs) cultured in a rotational oxygen-permeable bioreactor system (ROBS). Three-dimensionally (3D) printed beta-tricalcium phosphate (β-TCP) scaffolds with pore sizes of 500 µm and 1000 µm were seeded with pBMSC and cultured for 7 and 14 days under dynamic perfusion conditions. Gene expression analysis revealed significantly higher levels of osteogenic markers (Runx2, BMP-2, ALP, Osx, Col1A1) in the 1000 µm group, particularly at the early time point, with the later-stage marker Osteocalcin (Ocl) rising faster and higher in the 1000 µm group, after a lower expression at 7 days. ALP activity assays corroborated these findings. Despite having lower mechanical strength, the 1000 µm scaffolds supported a homogeneous cell distribution and high viability across all regions. These results suggest that larger pore sizes enhance early osteogenic commitment by improving nutrient transport and fluid flow in dynamic culture. These findings also support the use of larger-pore scaffolds in bioreactor-based preconditioning strategies and underscore the clinical importance of promoting early osteogenic differentiation to reduce in vitro culture time, an essential consideration for the timely preparation of implantable grafts in bone tissue engineering.