Purpose: Footwork speed is closely linked to explosive strength, and both percentage- (PBRT) and velocity-based resistance training (VBRT) are popular methods for developing muscle strength. This study aimed to compare the effects of PBRT and VBRT on lower limb explosive power and footwork movement speed in elite university badminton players over a 6-week training period. Methods: A total of 20 elite badminton players (12 males, 8 females) from Tongji University were randomly divided into VBRT (n = 10) and PBRT groups (n = 10). The VBRT group trained with loads determined by target speed and velocity loss, while the PBRT participants used fixed loads based on a percentage of their one-repetition maximum (1RM). Both the groups performed free-weight back squats with relative loads ranging from 65% to 95% of 1RM over 6 weeks. The pre- and post-training measurements included back squat 1RM; countermovement (CMJ), squat (SJ), and standing long jumps (SLJs); self-weighted squat jump speed (SJS); left and right touch line (LRF), full-field four-point (FF), and front and back touch net footwork (FBF). Results: (1) The baseline measurements showed no significant differences between the groups (p > 0.05). (2) Post-training, both VBRT and PBRT improved the participants’ lower limb explosive power and footwork movement (p < 0.05). (3) The VBRT group demonstrated significantly greater improvements than the PBRT group in all the measures (p < 0.05). Conclusions: VBRT was superior to PBRT in boosting lower limb explosive power and footwork speed in badminton players over 6 weeks, leading to more significant strength–related and neural adaptations.