Objective To establish the 3D hydrogel cell model and apply compressive stress with different intensities, frequencies and durations on osteoclasts, so as to observe the effect of compressive stress on osteoclast differentiation and investigate the appropriate compressive stress solution for inhibiting osteoclast differentiation. Methods M-CSF and RANKL were used to induce bone marrow mononuclear cells into osteoclasts. After the 3D cell-agarose mixture was seeded in compression culture plate, compressive stress was applied on osteoclasts with different intensities, frequencies and durations the next day. The cells in control group were not interfered. The cells were divided as following: G0 (control group), G1 (1%, 0.5 Hz, 4 h), G2 (2%, 0.5 Hz, 4 h), G3 (3%, 0.5 Hz, 4 h), G4 (1%, 1.0 Hz, 4 h), G5 (2%, 1.0 Hz, 4 h), G6 (3%, 1.0 Hz, 4 h). After the loading plan with the most effective intensity and frequency was calculated by statistical analysis, compressive stresses were applied on cells with different durations as following: D1(4 h), D2(8 h), D3(12 h), D4(16 h), and each group had two samples. Once compressive loading was finished, the total RNA extraction from cell-gel constructs were performed and Ctsk mRNA, NFATc1 mRNA, TRACP mRNA, M-CSF mRNA and RANK mRNA were measured by quantitative testing. Results RANK and TRACP mRNA expression significantly depended on intensities and frequencies of the compressive stress (P<0.01), and Ctsk mRNA significantly depended on intensities(P<0.01) while it differed notably with different frequencies (P<0.01). M-CSF mRNA expression with 8 h was much lower than that with 12 h (P<0.01) and 16 h (P<0.05). RANK mRNA expression with 8 h was lower than that with 12 h (P<0.05) and 16 h (P<0.01). In addition, Ctsk and NFATc1 mRNA expression with 16 h was higher than that with 4 h and 8 h (P<0.05). Conclusions In the 3D hydrogel model, 1% intensity, frequency of 0.5 Hz, cyclic compression intervention with 8 h can suppress the differentiation of osteoclasts. The research findings provide the theoretical basis for preventing osteoporosis and improving the peak bone mass by appropriate exercise.