Matrix viscoelastic properties have been shown to have important effects on cell functions. However, the conventional culture methods for investigating the influences of viscoelastic properties on cell functions cannot exclude the influence of cell morphology. Therefore, in this study, cell morphology was well-controlled by using micropatterns, and the influences of the viscosity of the cell culture medium on cell functions under controlled cell morphology were investigated. Human bone marrow-derived mesenchymal stem cells (hMSCs) were cultured on circular micropatterns of different sizes and elliptic micropatterns of different aspect ratios to control cell size and elongation. The cells were cultured in viscous media of different viscosities, and their osteogenic and adipogenic differentiation were compared. Viscosity could affect the osteogenic and adipogenic differentiation of hMSCs, and the effect was dependent on cell morphology. High viscosity induced a promotive effect on the osteogenic differentiation and an inhibitory effect on the adipogenic differentiation of large and elongated hMSCs. However, viscosity did not affect the osteogenic or adipogenic differentiation of small hMSCs. The effects were correlated with its influence on the actin filament organization of the hMSCs on the micropatterns. The results provide useful information for controlling stem cell functions and tissue engineering.