Work zones widely exist on urban roads in many countries and have a significant negative impact on traffic. Few studies have focused on modeling the traffic flow of the work zone on the urban arterials, especially on the work zone at the intersections. In this paper, a microscopic model based on the social force theory for the traffic flow of the intersection with a specific work zone, called straddling work zone, is proposed. The model can capture the no lane division and irregular boundary characteristics of the traffic of the intersection with a straddling work zone and also can reflect the interaction of the intersection traffic flows from the two opposite directions. The proposed model is calibrated and validated using the real work zone data, and the results display that the MARE values are all less than 10%. The factors affecting the traffic flow in the straddling work zone are analyzed through simulation. This study reveals that the distance from the lower edge of the work zone to the median divider of the road and the proportion of large vehicles in the work zone have the greatest impact on the signalized intersection, which provides a reference for the future traffic control at the intersection with the straddling work zone.