A virtual universal serial bus (USB) flash memory storage device with a peripheral component interconnect (PCI) Express including a microcontroller connected separately to a flash memory and PCI Express connecting interface, and the microcontroller has a flash memory interface, a PCI Express interface and a virtual USB module and the virtual USB module includes a USB host and a USB device. If a host gives a USB instruction for saving or reading to the storage device, the USB instruction will be sent to and executed by the virtual USB module and the required data processing for saving or reading will be completed through the flash memory interface and the flash memory. The data in the storage device can be transmitted with a PCI Express standard transmission rate, and the host considers the storage device as a USB device instead of a pure PCI Express device.