A working method for a smart card reader, which comprises that: the card reader is powered on and initialized; a system mode is set according to a type of a device which connects to the card reader, and determines the system mode; if the system mode is an APPLE® mode, determine whether an APPLE® authenticating operation is required to be re-performed, if the APPLE® authenticating operation is required to be re-performed, perform the APPLE® authenticating operation, waiting for receiving APPLE® data sent by an APPLE® device, the card reader performs corresponding operation in accordance with a type of an instruction; if the system mode is a USB mode, determine whether a USB data transmission flag is set, enable a USB connection and perform a USB enumeration in a case that the USB data transmission is not set, and when the USB enumeration is finished, the USB data transmission flag is set; waiting for receiving a USB data sent by the upper computer in a case that the USB data transmission flag is set, the card reader performs corresponding operation according to the type of the instruction. The present disclosure realizes that the card reader can communicate with not only an upper computer but an iPhone 5 via a USB interface or a lighting interface respectively.