Fractal dimension (Df) is an index to describe the irregular continuous structure by quantifying the complexity. The concept of fractals has been employed to describe the complicated structure of polymer gel and human tissue. This study examined the effect of Df on cell proliferation and stem cell differentiation in six polymer hydrogels with Df ranging from 1.2 to 2.1. It was observed that fibroblasts and mesenchymal stem cells (MSCs) grew faster in hydrogels with higher Df. Moreover, hydrogels with a fractal structure of Df ≤ 1.4, ≥1.6, and ≥1.8 promoted the neural, osteogenic, and chondrogenic differentiation of MSCs, respectively. The fractal structure of gel can modulate cell proliferation and fate, which provides an insight into designing the appropriate fractal and molecular structure of polymer hydrogel for biomedical applications.