Purpose: Investigate the effect of 6 weeks of complex training with different training order on the maximum lower body isokinatic strength, 5×6s interval cycling, and muscle damage in collegiate male basketball athletes. Methods: Twenty Division I male basketball players of CCU (age: 19±1.5 yr, height: 181.1±9.18 cm, weight: 80.0±12.97 kg, VO(subscript 2max): 57.0±6.27 m^(-1)•kg^(-1)•min^(-1)) were randomly assigned into WP (weight training followed by plyometric training) and PW (plyometric training followed by weight training) group. Both group received two 60-min training session per week for 6 weeks. Pre and post test were carried out before and after 6 weeks of complex training. Data were analyzed by using one-way ANCOVA with α level set at .05. Results: The results indicated that after 6 weeks of complex training, both group revealed significant improvement in knee flexor at 60°& 180°•S^(-1) peak torque (60°•S^(-1):171.4±46.40 vs. 205.7±20.46; 180°•S^(-1):134.8±52.62 vs. 173.2±14.94 N•m), anaerobic peak power (14.0±1.80 vs. 14.6±1.51 W/kg) (p<.05). No significant difference was found in peak torque, creatine kinase and self-reported perceived muscle soreness scale between WP and PW. Conclusions: In conclusion, regardless of training order, complex training can help improve lower body strength, anaerobic power, and no significant difference was found in muscle damage between WP and PW.