Microtubule acetylation is known to promote autophagic degradation; however, its therapeutic potential in resolving exercise-induced autophagic flux blockage and facilitating injured muscle recovery remains unclear. In this study, Sprague-Dawley rats were treated with Tubastatin A for 3 consecutive days to enhance microtubule acetylation. Subsequently, the rats underwent a 90-minute downhill run at a gradient of -16°and a speed of 16 m·min⁻¹. Soleus muscles were sampled at 12 h post-exercise. Single muscle fibers were isolated and labelled with α-tubulin, acetylated α-tubulin (AcK40 α-tubulin), cytoplasmic dynein intermediate chain (dynein), or LC3 for immunofluorescent analysis. Protein expression of α-tubulin, AcK40 α-tubulin, dynein, LC3, p62, Myf5, Myod, and Myogenin were detected by Western blot. The results showed that Tubastatin A treatment significantly upregulated the expression of AcK40 α-tubulin and dynein. It also increased the amount of dynein on α-tubulin and promoted the retrograde transport of autophagosomes. In response to downhill running, Tubastatin A-treated rats exhibited enhanced autolysosome formation, along with reduced LC3-II and p62 expression. Additionally, Tubastatin A further potentiated the increases in MyoD and Myogenin induced by downhill running. These findings suggest that enhancing microtubule acetylation through Tubastatin A can mitigate the impairment of autophagosome degradation caused by downhill running and promote the myogenic program in skeletal muscle.