Although numerical models on the shoulder complex joint are currently available, many are impractical because of the procedural complexity coupled with limited and mere simple simulations. The present study defined the clavicle-scapula system as the “base of the humerus” in determining the position of proximal head of humerus, rendering conclusive innovation of a six degree of freedom (DOF) shoulder complex joint model. Furthermore, a complete measurement system where evaluation by calibrating the actual values via the use of an electromagnetic tracking device (ETD) was developed based on the innovated model. The special calibration method using optimizing calculation to work out the rotational center of humerus was employed and actually tested if the theoretical consideration was practically available. As a result of accuracy check experiments, the measurement error was defined within 2-3 mm, indicating sufficient accuracy in studies for human movement. Our findings strongly advocate that the benefit of this novel measurement system would contribute to studies related to shoulder movements in physiological anthropology.