Objective To investigate the effect of circadian rhythm disorder on rat knee cartilage and the mechanism of basic helix-loop-helix ARNT like 1 (Bmal1) on the regulation of cell cycle-related genes. Methods Forty rats were randomly divided into normal group, circadian rhythm disorder group (disorder group), Bmal1 overexpression lentivirus infection circadian rhythm disorder group (Bmal1 up-regulated group) and Bmal1 overexpression lentivirus negative infection circadian rhythm disorder group (Bmal1 negative infection group), with 10 rats in each group. Saffron fast green staining, TdT-mediated dUTP nick-end labeling staining, immunohistochemical staining, reverse transcription polymerase chain reaction and Western blotting were used to compare the pathological changes of cartilage tissue, the apoptosis of chondrocytes, and the relative mRNA expression levels of Bmal1, WEE1 G2 checkpoint kinase (Wee1), cyclin-dependent kinase 1 (Cdk1), cyclin B1 (Ccnb1), BCL2-associated X protein (Bax), apoptosis regulator 2 (Bcl2), interleukin 1 (Il1), interleukin 6 (Il6), tumor necrosis factor (Tnf) and matrix metallopeptidase 13 (Mmp13) among different groups. The relative expression levels of BMAL1, WEE1, CDK1, CCNB1, BAX and BCL2 proteins were detected, and correlation analysis was performed according to the relative expression of mRNA. Results Safranine fast green staining showed that the thickness of cartilage matrix in the normal group was normal and uniform red. The cartilage matrix in the disorder group and the Bmal1 negative infection group was destroyed, and the proteoglycan was lost obviously, showing uneven red. The thickness of cartilage matrix in the Bmal1 up-regulated group was basically normal, and the proteoglycan was not lost obviously, and the red was slightly less uniform. Compared with those of the normal group, the positive rates of apoptotic cells in articular cartilage of the disorder group and the Bmal1 negative infection group increased significantly, the mRNA and protein expression levels of Bmal1, Wee1, and Bcl2 were down-regulated, the mRNA and protein expression levels of Cdk1, Ccnb1, and Bax were up-regulated, the mRNA expression levels of Il1, Il6, Tnf and Mmp13 were up-regulated, the differences were statistically significant (P<0.05); there was no significant change in the positive rate of apoptotic cells in the articular cartilage of the Bmal1 up-regulated group, and there was no significant difference in the mRNA or protein expression of Bmal1, Wee1, Bcl2, Cdk1, Ccnb1 or Bax, nor the mRNA expression of Il1, Il6, Tnf or Mmp13 (P>0.05). Correlation analysis showed that Bmal1 was positively correlated with Wee1 and Bcl2 (r=0.84, 0.44; P<0.01), and negatively correlated with Cdk1, Ccnb1 and Bax (r=–0.55, –0.72, –0.41; P<0.01). Conclusion Chronic circadian rhythm disorder can cause the increase of chondrocyte apoptosis and osteoarthritis-like changes of articular cartilage through the expression changes of circadian clock gene Bmal1 and cell cycle-related genes and proteins.