Objective To explore the effects of low-intensity pulsed ultrasound (LIPUS) on anabolism, apoptosis and intraflagellar transport 88 (IFT88) expression in mouse chondrocytes after interleukin (IL)-1β intervention, and the correlation of cartilage repairment by LIPUS with primary cilia. Methods IL-1β intervention, LIPUS intervention and lentiviral carrying IFT88-specifific short hairpin RNA (sh-IFT88) transfection were performed on mouse chondrocytes, respectively. The groups included: normal chondrocyte group (N group), chondrocyte after IL-1β intervention group (OA group), chondrocyte after IL-1β intervention+LIPUS group (OA+U group), sh-IFT88+IL-1β intervention chondrocyte group (KO+OA group), and sh-IFT88+LIPUS+IL-1β treated chondrocyte group (KO+OA+U group). Real-time polymerase chain reaction and immunofluorescence were used to determine the expression of collagen Ⅱ, aggrecan, and primary cilia, and apoptosis was measured by flow cytometry. All experimental data were statistically analyzed using the GraphPad Prism 9.5 software. Results The expression of collagen Ⅱ and aggrecan increased, the apoptosis decreased, and the incidence of primary cilia in chondrocytes of mice increased in the OA+U group compared with those in the OA group (P<0.05). The collagen Ⅱ and aggrecan expression decreased and the apoptosis increased in the KO+OA+U group compared with those in the OA+U group (P<0.05). Conclusion LIPUS can reduce the apoptosis of chondrocytes in C57 mice after IL-1β intervention, and increase the expression of collagen Ⅱ and aggrecan in chondrocyte matrix, and the effect is related to primary cilia.