The aim of this study was to investigate the morphological and microstructural alterations of the articular cartilage and bones during treadmill exercises with different exercise intensities. Sixty 5-week-old female rats were randomly divided into 10 groups: five additional weight-bearing groups (WBx) and five additional weight-bearing with treadmill exercise groups (EBx), which were subjected to additional weight bearing of x% (x = 0, 5, 12, 19, and 26) of the corresponding body weight of each rat for 15 min/day. After 8 weeks of experiment, the rats were humanely sacrificed and their bilateral intact knee joints were harvested. Morphological analysis of the cartilages and microcomputed tomography evaluation of bones were subsequently performed. Results showed that increased additional weight bearing may lead to cartilage damage. No significant difference was observed among the subchondral cortical thicknesses of the groups. The microstructure of subchondral trabecular bone of 12% and 19% additional weight-bearing groups was significantly improved; however, the WB26 and EB26 groups showed low bone mineral density and bone volume fraction as well as high structure model index. In conclusion, effects of treadmill exercise on joints may be associated with different additional weight-bearing levels, and exercise intensities during joint growth and maturation should be selected reasonably.