Currently, an increasing number of people are suffering from fatigue due to the state of their lifestyles, such as sedentary work in a relatively small space, irregular sleep patterns, or the lack of movement and exercise. The present study was designed to simulate the occurrence of fatigue in the above populations through a chronic restraint stress (CRS) model, and to reveal its dynamic processes and potential underlying molecular mechanisms. ICR mice were subjected to 8 h of restraint stress each day for 5, 10, or 15 days. It was found that the weight-loaded swimming performance, grip strength, and locomotor activity of the mice all decreased under CRS treatment, and that up to 15 days of CRS induced notable fatigue. Gastrocnemius muscle atrophy and some abnormal biochemical parameters related to fatigue under CRS were observed. Furthermore, transcriptome data showed that the changes in muscle cell metabolism and mitochondrial dysfunction were associated with the AMPK signaling pathway in CRS-treated mice. Western blotting analysis of the AMPK/PGC-1α signaling pathway revealed that CRS could decrease mitochondrial biogenesis and reduce the numbers of type I skeletal muscle fibers in the gastrocnemius of mice. CRS could also block the protective mitophagic flux to inhibit the abnormal clearance of damaged mitochondria. Our study suggests a critical link between muscle atrophy and CRS-induced fatigue in mice, suggesting that the pharmacological promotion of muscle and mitochondrial function can be used as a treatment for stress-induced fatigue.