The present invention discloses a virtual universal serial bus (USB) card reader with a peripheral component interconnect (PCI) Express interface. The card reader includes a microcontroller connected to a PCI Express connecting interface and a memory card connecting interface separately. The microcontroller includes a memory card interface, a PCI Express interface and a virtual USB module. The virtual USB module includes a USB host and a USB device. If a host gives an instruction to a memory card connected to the card reader for storing or reading data, the instruction will be sent to and executed by the virtual USB module. The data in the memory card can be transmitted at a transmission rate up to the USB standard, and the host will consider the card reader as a USB device instead of simply a PCI Express device.