In the semiconductor wafer fabrication system, for re-entrant batch processing machine with distinct due window and incompatible families, the scheduling problem is known to be NP-complete. Three-phase rolling mixed integer linear programming algorithm is proposed. According to time-sequence-based and event-based combined decomposition strategy, the whole simulation time is decomposed into different rolling horizons. A horizon is corresponding to a sub-problem. Each sub-problem is divided into three phases：Sequencing, dispatching and updating. The real-time scheduling simulation platform and mixed integer linear programming are used to solve dispatching, updating, rolling and sequencing, respectively. 6 representative examples are conducted. The results show that family-oriented three-phase rolling mixed integer linear programming algorithm can obtain better solutions in less computation time.