The contemporary prevalence of car ownership has presented urban intersections with burgeoning challenges in terms of motorisation and congestion. Traditional signal timing schemes often encounter difficulties in handling the resulting vehicle conflicts within the physical area of the intersection. Accordingly, an intersection traffic signal timing method based on the intersection physical zone traffic status (IPAT-ATS) is proposed in this study. Different types of intersection anomalies are defined based on the impact of various abnormal vehicle operating states on vehicle flow in each entrance and exit lane. Using a traffic efficiency model, the flow state of intersections under different abnormal states is analysed to allocate traffic flows optimally, thereby maximising traffic efficiency under various abnormal states. The proposed method undergoes testing through simulations at the Weidi Road and Youyi Road intersection in Tianjin, China. Compared with the current signal timing scheme, this method significantly enhances the intersection efficiency for different traffic anomalies.