To accurately depict the characteristics of microscopic motion, and describe two-dimensional movements of non-motorized traffic flow, the comfort-zone theory was put forward for the first time to describe the generation of behavior motivation of cyclists. Besides, based on this new theory, we proposed a three-layered model to describe the movements of non-motorized vehicles from the whole process of behaviors. Comparing with empirical data collected in a physically separated road section in Shanghai and the social force model, the proposed model can reflect the microscopic features better, and the average error of trajectories is only 0.64 m.