Perturbation exercises enhance lower limb and trunk muscles, and adding swing perturbation while loading during exercise might improve muscle activation or strength. This study aimed to check variations in trunk and lower limb muscle activity during conventional isometric squats, and whether it will change with or without swing using the Hammerobics-synchronized squat method. Twelve healthy men participated in this study. Activities for the abductor hallucis, tibialis anterior, tibialis posterior, peroneus longus, rectus femoris, biceps femoris long head, semitendinosus, gluteus maximus, multifidus, and internal oblique muscles were measured using surface electromyography during a Hammerobics-synchronized squat and conventional isometric squat. Muscle activities were statistically compared between squat methods. Hammerobics-synchronized squats significantly activated the abductor hallucis, tibialis anterior, tibialis posterior, peroneus longus, semitendinosus, and multifidus muscles, in both phases, compared with the conventional isometric squats. The Hammerobics-synchronized squat exercise can be considered for trunk and foot stability exercise.