Bone and joint injuries are common motor system diseases that seriously affect the quality of life of patients. This study aims to explore the promoting effect of protein polysaccharide molecules combined with exercise on bone and joint injury repair, as well as the underlying protein kinase signaling pathway mechanism. Research on constructing protein polysaccharide complexes through molecular docking technology to analyze their construction characteristics and the properties of protein kinases. By constructing relevant signaling pathways and applying support vector machine technology, the potential signaling pathways of kinases were encoded and calculated for predictive analysis. Subsequently, the repair effect of bone and joint injuries was quantitatively evaluated by combining exercise methods. The research results indicate that the constructed protein polysaccharide complex can effectively activate related protein kinase signaling pathways, enhance the repair effect of bone and joint injuries. Through the combination of exercise methods, the healing time of bone injuries is significantly shortened, and the recovery of joint function is significantly improved. Therefore, the binding movement of protein polysaccharide molecules has a significant effect on promoting the repair of bone and joint injuries, and its mechanism of action is mainly achieved by activating the signaling pathways of specific protein kinases.