In order to effectively control traffic flow and give priority to transit, a phase sequence-changeable real-time rolling horizon optimization model is proposed for isolated intersection signal controlling. The model embeds transit priority in optimization control and assigns a weighting factor in real time to every bus. The model optimizes the phase sequence and phase length with the aim of minimizing the average passenger delay of both transits and the general vehicles at the intersection. The phase sequence optimization is realized through jumping phase. The model is solved by using an improved genetic algorithm. Applied result shows that the phase sequence-changeable real-time rolling horizon optimization model can effectively reduce the average passenger delay of system, and can prioritize transit vehicles while minimizing the impact on the general vehicles.