A wafer transfer system includes a bidirectional wafer carrying pod, an over-head transport (OHT) rail, an OHT, two platforms, and two loading ports respectively connected to the two platforms. The bidirectional wafer carrying pod has a loading housing and two doors respectively and detachably installed on the two opposite sides of the loading housing. The OHT rail has a single rail section and a double rail section. The two ends of the double rail section are connected to the single rail section. The platforms are respectively disposed beside the double rail section. The loading ports are disposed under the double rail section. Through the OHT, The bidirectional wafer carrying pod can selectively be transferred to one rail of the double rail section and disposed on the loading port of the tool corresponding to the one rail of the double rail section.