The present invention relates to a PCIe switch apparatus and a method of controlling the connection thereof. The PCIe switch apparatus includes a PCIe photoconversion unit for converting an electrical signal input from a local host into packet data and converting the converted packet data into an optical signal. A PCIe slot board unit reconverts the optical signal into the packet data, reconverts the packet data into the electrical signal, and outputs the electrical signal to a PCIe-based device. An optical cable connects the PCIe photoconversion unit and the PCIe slot board unit to each other. The PCIe switch apparatus controls a long-distance communication interface between the local host and the PCIe-based device.