Background: The study explored the influence of repeated drop jumps (DJs) from different drop heights on the lower extremity bilateral asymmetry and muscle activation of countermovement jumps (CMJs). Methods: Eighteen male athletes performed 200 drop jumps (DJs200) from three drop jump height (DJH30, 40 and 50 cm). The CMJs were performed before the first DJ and after the 50th, 100th, 150th and 200th DJs, recording them as pre-CMJ, CMJs50, CMJs100, CMJs150 and CMJs200. One-way repeated measures ANOVA was used to compare differences among the three drop heights at pre-CMJ, CMJs50, CMJs100, CMJs150 and CMJs200, respectively. Results: The peak ground reaction forces (PGRF) of CMJs100, CMJs150 and CMJs200 at DJH50 were greater than at DJH30 and DJH40 (all p < 0.05). The muscle activation during CMJs50 at DJH50 was greater than at DJH30 and DJH40 (all p < 0.05). The muscle activation during CMJs100, CMJs150 and CMJs200 at DJH50 was smaller than at DJH40 and DJH30 (all p < 0.05). The PGRF had no significant difference among the three different drop heights during CMJs50 (p > 0.05). Conclusions: The DJs50 at DJH50 had no effect on the bilateral asymmetry and increased muscle activation of CMJs. The excessive DJs100 at DJH50 increased bilateral asymmetry and decreased CMJ muscle activation during CMJs.