Considering the strong human disturbances of urban rivers, 10 evaluation indexes from three dimensions of horizontal integrity, longitudinal integrity and vertical integrity were selected. The traditional grey clustering evaluation method was improved by introducing information entropy to construct the urban river physical integrity evaluation index system. This method was used to evaluate the physical habitat integrity of Liangshui River in Beijing. The results show that: among the 21 monitoring sites under the evaluation of physical habitat integrity, evaluation results were defined to be four grades of good, better, medium and poor, accounting for 19. 1%, 23. 8%, 33. 3% and 23. 8%, respectively. The indicators leading to poor physical habitat integrity of Liangshui River are the low ecological flow(EF), longitudinal connectivity(LC), and river meandering(RM)in sequence. The prominent reasons that cause poor physical habitat integrity of Liangshui River attribute to low ecological flow, more dams and unreasonable land use. The periodicity of the emerging dam is consistent with the same of the physical habitat deterioration.