Since last decade, the cluster tool has been mainstream in modern semiconductor manufacturing factories. In general, the cluster tool occupies 60% to 70% of production machines for advanced technology factories. The most characteristic feature of this kind of equipment is to integrate the relevant processes into one single machine to reduce wafer transportation time and prevent wafer contaminations as well. Nevertheless, cluster tools also increase the difficulty of production planning significantly, particularly for shop floor control due to complicated machine configurations. The main objective of this study is to propose a short-term scheduling model. The noteworthy goal of scheduling is to maximize the throughput within time constraints. There are two modules included in this scheduling model—arrival time estimation and short-term scheduling. The concept of the dynamic cycle time of the product’s step is applied to estimate the arrival time of the work in process (WIP) in front of machine. Furthermore, in order to avoid violating the time constraint of the WIP, an algorithm to calculate the latest time of the WIP to process on the machine is developed. Based on the latest process time of the WIP and the combination efficiency table, the production schedule of the cluster tools can be re-arranged to fulfill the production goal. The scheduling process will be renewed every three hours to make sure of the effectiveness and good performance of the schedule.