Objective To quantify the lower limb muscle synergy characteristics of athletes during the abdominal take-off phase before and after exercise-induced fatigue (EIF) and reveal the impact of EIF on the lower limb muscle synergy characteristics of athletes during the abdominal take-off phase. Methods The surface electromyographic data of the lower limbs during the abdominal take-off phase of 10 second-level male athletes in track and field special classes before and after EIF intervention were compared. Muscle synergy structures were analyzed before and after EIF. The paired sample t-test was used to compare the differences in synergy parameters before and after EIF. Results Two synergistic elements were extracted before and after EIF, and alternate activation of the muscle synergy structures was observed. After EIF, the degree of activation of synergy element 2 decreased significantly from 53.21 ± 7.90 to 43.44 ± 10.23. However, there was no significant change in synergy element 1. After EIF, the contribution of the rectus femoris muscle of synergy element 1 significantly increased from 0.37 ± 0.04 to 0.44 ± 0.07, and the contribution of the semitendinosus muscle decreased significantly from 0.13 ± 0.05 to 0.08 ± 0.05. Conclusions During abdominal take-off, as fatigue increases, the activation degree of the synergistic elements of each lower limb muscle decreases, and the contribution of the rectus femoris muscle in the synergy element to absorb the ground reaction force increases. This indicates that the rectus femoris muscle is at risk of sprain, and prevention of rectus femoris muscle injury should be strengthened.