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This paper describes a real-time transfer control method to produce a high throughput for linear tools of semiconductor manufacturing equipment. We developed a transfer control method for various process times with two steps during operation of the equipment. The first step uses a local search to find a transfer sequence producing a high throughput in advance for various process times, and the second step switches between transfer sequences during the operation of the equipment by referring to a decision tree made from the results of the first step. The method calculates the transfer sequence in a time period from recognizing the process time to the start of transferring the wafer and improves the throughput of linear tools in more than 60% of the tested process time combinations. In the most improved case, the throughput improved by 53%.