We constructed a three-dimensional whole-body musculoskeletal model of the Japanese macaque (Macaca fuscata) based on computed tomography and dissection of a cadaver. The skeleton was modeled as a chain of 20 bone segments connected by joints. Joint centers and rotational axes were estimated by joint morphology based on joint surface approximation using a quadric function. The path of each muscle was defined by a line segment connecting origin to insertion through an intermediary point if necessary. Mass and fascicle length of each were systematically recorded to calculate physiological cross-sectional area to estimate the capacity of each muscle to generate force. Using this anatomically accurate model, muscle moment arms and force vectors generated by individual limb muscles at the foot and hand were calculated to computationally predict muscle functions. Furthermore, three-dimensional whole-body musculoskeletal kinematics of the Japanese macaque was reconstructed from ordinary video sequences based on this model and a model-based matching technique. The results showed that the proposed model can successfully reconstruct and visualize anatomically reasonable, natural musculoskeletal motion of the Japanese macaque during quadrupedal/bipedal locomotion, demonstrating the validity and efficacy of the constructed musculoskeletal model. The present biologically relevant model may serve as a useful tool for comprehensive understanding of the design principles of the musculoskeletal system and the control mechanisms for locomotion in the Japanese macaque and other primates.