The aim of modeling musculoskeletal systems is to understand the mechanisms of locomotion control in terms of neurophysiology and neuroanatomy. The complexity and unique nature of neuromuscular systems, however, make control problems in these systems very challenging due to several characteristics including speed and precision. Thus, their investigation requires the use of simple and analyzable methods. Consequently, taking into account the central pattern generator’s (CPG) function, we attempted to create a structured chaotic model of how human joints and muscles interact for the purpose of facilitating gait and rehabilitation in patients with incomplete spinal cord injury. The four muscle groups used in this model are gluteus, and hip flexor groups for flexion and extension of the hip joints as well as hamstring muscles and vasti muscles for flexion and extension of the knee joint. The results indicate that the output of the chaotic model of muscle and joint interactions in a healthy state would be chaotic, while in the incomplete spinal cord injury state, it would remain a fixed point. For model rehabilitation, afferent nerve stimulation is used in a CPG model; based on the modeling results, by applying coefficients of 1.98, 2.21, and 3.1 to the values of Ia, II, and Ib afferent nerves, the incomplete spinal cord injury model state is changed from a fix-point to periodic in a permanent fashion, suggesting locomotion with rehabilitation in our model. Based on the results obtained from the chaotic model of muscle and joint interactions as well as the comparisons made with reference papers, it can be stated that this model has acceptable output while enjoying simple computations and can predict different norms.