Objective The purpose of this study was to examine the effect of shoe cushioning on impact characteristics and kinematics of lower extremities under fatigue conditions during drop landings. Methods Fifteen trained male athletes were required to execute three successful trials of drop landings from a 60-cm platform before and after fatigue protocol. The variables included impact force, loading rate, lower extremity kinematics, joint mechanics, stiffness in the sagittal plane movement. Results Highly-cushioned shoe reduced the loading rate at heel in pre-fatigue (389.67 vs 688.03 BW·s-1), and the time to peak loading rate of heel was significantly shorter than control shoes (29.9 vs 36.63 ms). In post-fatigue: 1) the peak impact force (3.77 vs 4.5 BW) and loading rate at heel (375.51 vs 756.8 BW·s-1), loading rate at forefoot (193.17 vs 265.05 BW·s-1) were significantly reduced of highly-cushioned shoe. Meanwhile the time to peak impact force (forefoot: 12.77 vs 10.07 ms, heel: 41.56 vs 35.46 ms) and peak loading rate of heel (36.41 vs 29.9 ms) were significantly longer of highly-cushioned shoe. 2) Besides, the contact (131.69° vs. 126.51°) and minimum angle (86.97° vs. 84.72°) of ankle were significantly greater of highly-cushioned shoe. 3) No significant changes were found in lower extremity stiffness, peak moment and joint stiffness of ankle. Conclusion Shoe cushioning only make a limited contribution to reducing impact forces before fatigue, while wearing a highly-cushioned shoe can significantly reduce the peak impact force and loading rate during landing in post fatigue. It suggested that in the situation where neuromuscular activity is reduced or absent, highly-cushioned shoe can effectively attenuate the impact, thereby helping to avoid/reduce the potential impact damage after fatigue.