The present invention provides a scheduling method for a peripheral component interconnect express (PCIe) switch of an electronic system. The PCIe switch is utilized for handling input/output requests of a host of the electronic system. The scheduling method includes the PCIe switch determining a scheduling sequence of message signal interrupts (MSIs) and read/write requests corresponding to the input/output requests according to amount of the message signal interrupts corresponding to the input/output requests; and the PCIe switch handling the message signal interrupts and the read/write requests according to the scheduling sequence.