Objective Screening for differentially expressed genes (DEGs) in anterior tibial muscle of rats and pathway analysis after chronic intermittent hypoxia and acute hypoxia exposure. Methods Twenty-four SD rats were randomly divided into the normoxia control group (C group), the chronic intermittent hypoxia group ( IH group, 12. 4% O2 , 8 h / d, 4 weeks) and the acute hypoxia group (AH group, 12. 4% O2 , 24 h / d, 3 d). The grasping force and lean body weight were examined after the interventions. The anterior tibial muscle (TA) fiber cross-sectional area (FCSA) was examined by hematoxylin / eosin staining. Relative protein expression levels of Atrogin-1 and muscle RING-finger protein-1 (MuRF1) were examined by western blotting. Total RNA of TA was extracted and sequenced, DEGs were screened, and the biological process (BP) and pathways enriched by DEGs were analyzed. Results (1) During the intervention, body weights of the IH group were lower than those of the C group at each time point, and the body weight of AH group continued to decrease. After the intervention, the lean body weight and relative grip in the AH group were significantly lower than in the C group (P< 0. 05). (2) The morphology of muscle fibers of the TA was destroyed in the IH and AH groups, and was more obvious in the IH group, but there were no significant differences in FCSA. (3) The levels of Atrogin-1 and MuRF1 in TA in the IH group were significantly higher than those in the C group, and the MuRF1 level in the AH group was significantly higher than the C group ( P< 0. 05). ( 4) The DEGs up-regulated in AH/ C group comparison but down- regulated in the IH/ C group comparison were slow muscle structure-related genes. Gene Ontogeny and KEGG analysis showed that the DEGs in the IH/ C group were mainly enriched in peroxisome proliferator-activated receptor signaling pathway and other pathways. The function of up-regulated DEGs was mainly concentrated in the process of antioxidant and glycolipid metabolism, and for down-regulated genes were concentrated in the processes of transformation between fast and slow muscles and oxidative stress. The functions of up-regulated DEGs in the AH/ C group were mainly concentrated in oxidative stress, inflammatory response and transformation between fast and slow muscles, and for the down-regulated DEGs were concentrated in Smad protein signal transduction and ubiquitin protein ligase binding. Conclusions The DEGs of AT of rats affected by chronic intermittent hypoxia and acute hypoxia were enriched for processes in glycolipid metabolism and promoting oxidative stress and inflammatory responses, respectively, suggesting that different hypoxia modes affect skeletal muscle metabolism through different pathways.