To study whether ACT exerts anti-fatigue activity against CRF by inducing skeletal muscle mitophagy via suppressing PHD2 to upregulate the HIF-1α/BNIP3 signaling pathway. In this study, the molecular docking virtual screening technique was used to screen active components in Cistanche tubulosa that act as potential PHD2 inhibitors; the preliminary verification was carried out by Surface plasmon resonance (SPR) technology. BALB/c mice were treated with Paclitaxel (PTX, 10 mg/kg) and ACT (50, 100 mg/kg) alone or in combination for 20 days. Fatigue-related behaviors, energy metabolism and skeletal muscle mitochondria were assessed. Murine C2C12 myoblast was cultured and differentiated; then, a C26 tumor cell-conditioned medium was added to induce cachexia. Intracellular reactive oxygen species (ROS), mitochondrial membrane potential, mitochondrial microstructure and function, autophagy, PHD2/HIF-1 and PINK1/Parkin signal pathway proteins were analyzed. Then, interfering RNA technology was used to silence PHD2 and observe the efficacy of ACT. We demonstrated that ACT exerted good binding activity with PHD2; ACT administration ameliorated PTX-induced muscle fatigue-like behavior via improving muscle quality and mitochondria function, increasing mitophagy, upregulating COXIV, CytoC, PINK1, Parkin, HIF-1α and BNIP3 expression and inhibiting p62, LC3B, PHD2 and Beclin-1 expression. The protective effect of ACT disappeared after transfection with the PHD2 gene knockdown plasmid Egln-1-RNAi. These results suggest that ACT can improve CRF by promoting mitophagy via suppression of PHD2 to remove dysfunctional mitochondria, demonstrating that ACT has huge prospects for clinical application in CRF treatment.