Tissue-engineered bone scaffolds provide temporary mechanical support for bone tissue growth. Mechanical stimuli are transferred to seeded cells through the scaffold structure to promote cell proliferation and differentiation. This paper presents a numerical investigation specifically on bone and cartilage tissue differentiation with the aim to provide a theoretical basis for scaffold design and bone defect repair in clinics. In this study, the scaffold structures were established on the basis of cancellous bone microarchitectures. For finite element simulations, inlet velocity and compressive strain were applied under in vitro culture conditions. The influences of this scaffold morphology and macro-level culture conditions on micro-mechanical stimuli at scaffold surfaces were investigated. Correlations between the microarchitectural parameters and the mechanical parameters, as well as the cell differentiation parameters were analyzed. Highly heterogeneous stress distributions were observed on the scaffolds with irregular morphology. Cell differentiation on the scaffold was more sensitive to the inlet velocity than the axial strain. In addition, cartilage differentiation on the scaffolds with structures comprising more plate-like trabeculae was more pronounced than on those with more rod-like trabeculae. This paper is helpful to gain more insight into the mechanical environments under in vitro culture conditions that approximate the in vivo mechanical environments of Bone Marrow Stromal Cells (BMSCs).