Flywheel eccentric training is a type of training that combines concentric and eccentric contractions by creating inertial resistance with a flywheel device. This study compared the effects of high-intensity flywheel eccentric training and traditional barbell training on the anaerobic capacity and lower-limb strength of female college basketball players. Sixteen female Chinese University Basketball League (CUBAL) athletes from a university were recruited and randomly divided into flywheel eccentric training and traditional barbell training groups, with eight athletes in each group. They underwent two training sessions per week for 8 weeks. The athletes were assessed for their anaerobic capacity (blood lactate concentrations, peak anaerobic power, mean anaerobic power, fatigue index, 30-m sprint, T-test, and 17×15-m shuttle run), and lower-limb strength (1RM back squat, CMJ, peak power output (PPO), and isokinetic muscle strength) before and after the training intervention. After the training intervention, there was a significant difference between the flywheel eccentric training and traditional barbell training groups in each test index when compared to before and after the within-group experiment (P < 0.05). Between groups, there were significant differences in 3 min blood lactate concentrations (P < 0.05, d = 1.09), peak anaerobic power (P < 0.05; d = 1.10), mean anaerobic power (P < 0.05; d = 1.21), fatigue index (P < 0.05; d = 1.20), 30-m sprint (P < 0.05; d = 1.38), T-test (P < 0.05; d = 1.12), 17×15-m shuttle run (P < 0.05; d = 1.31), 1RM back squat (P < 0.05; d = 1.08), CMJ (P < 0.05; d = 1.11), peak power output (PPO) (P < 0.05; d = 1.26), and isokinetic muscle strength (P < 0.05). This study revealed that high-intensity flywheel eccentric training significantly enhanced the players’ anaerobic capacity and lower-limb strength and led to better performance than traditional barbell training across all measures.