Boots are widely used by many people for various purposes, but their impact on gait biomechanics and injury risk is not well understood. This study investigated the effects of boots on walking biomechanics, compared to casual footwear. The lower limb joint kinematics and kinetics of 20 healthy male participants aged 20 to 30 years old were compared during self-paced walking with boots and shoes. The results showed that walking with boots is associated with greater hip extensor (P = 0.009) and ankle dorsiflexor (P < 0.001) moments in early stance, hip power generation (P < 0.001) and knee power absorption (P < 0.001) in early swing phase, hip abductor (P < 0.001) and knee adduction (P < 0.001) moments in the entire stance, net concentric work for the hip joint in sagittal (13.9%, P = 0.001) and frontal (21.7%, P = 0.002) planes. In contrast, the subtalar supinator moment in the entire stance (P < 0.001), ankle angular velocity in late stance (P < 0.001), and net concentric (− 42.7%, P < 0.001) and eccentric (− 44.6%, P = 0.004) works of subtalar joint were significantly lower in the boot condition. The compensatory adjustments in the hip and knee joints may result from ankle restrictions. While boots may aid those with ankle disorders, lower limb loading and the risk of musculoskeletal injuries and osteoarthritis could be increased. This study offers new perspectives on the biomechanical impact of boots on gait, potential prevention and treatment strategies of related injuries, and advancing footwear design.