A method for a card reader to communicate with an upper computer comprises: initializing a card reader system and enabling an interrupt; determining an interrupt identification type; for Bluetooth communication interrupt identification resetting or USB communication interrupt identification resetting, receiving an instruction and saving a channel identification corresponding to the instruction, performing a corresponding operation according to an instruction type, sending a corresponding response to the upper computer and clearing the Bluetooth communication interrupt identification or the USB communication interrupt identification; for another interrupt identification, performing a corresponding operation according to an interrupt identification type. The method can solve a problem in prior art that a card reader cannot communicate with mobile devices of different models through a USB port.