Skeletal muscle atrophy is a common manifestation across various physiological and pathological conditions, severely impairing patients’quality of life and prognosis. In recent years, the gut microbiota, together with the "gut-muscle axis" it forms with the host, has been recognized as a critical factor influencing skeletal muscle homeostasis. Gut dysbiosis can promote muscle atrophy through multiple pathways, including disruption of the intestinal barrier, induction of chronic inflammation, and alterations in the spectrum of metabolites. Exercise is an effective strategy for maintaining skeletal muscle mass and function, and it has also been demonstrated to significantly modulate the composition and function of the gut microbiota. Increasing evidence suggests that exercise may exert beneficial effects on skeletal muscle atrophy via the gut-muscle axis by modulating the gut microbiota. This article aims to review the mechanistic role of the gut-muscle axis in skeletal muscle atrophy and the impact of exercise on the gut microbiota, with a specific focus on exploring the potential mechanisms and clinical evidence regarding how exercise mediates gut microbiota changes to ameliorate skeletal muscle atrophy. A comprehensive understanding of this complex interaction network will provide novel insights for developing prevention and treatment strategies for muscle atrophy based on exercise and gut microbiota interventions.