Non-obstructive particle damping (NOPD) is a new composite damping technology based on traditional partical damping and impacting damping, and it has good vibration-reduced results. Through studying thermodynamics constraint condition for non-inverse variation of inner tissue structure of the material, the endochronic theory obtained variation regularity of inner variable, further gave out evolution path of specific non-inverse thermodynamics variable under specific condition, and thus the constitutive relationship of the material was obtained. Based on endochronic theory, an incremental form of the endochronic constitutive relationship of discrete particle was derived, and then penalty element was introduced to solve the connection problem between structure and discrete particle, lastly finite element dynamics equation of NOPD composite structure was constructed. Based on the model of NOPD composite structure, simulation and experiment for response of NOPD free beam were made. It indicated that applying endochronic theory to analyze the response of NOPD is rational, which supplied an effective method for engineering application of NOPD.