The invention relates to a cross-debugging method of embedded system. The cross-debugging method comprises the following steps that S1, electrified starting is performed, and an operating system is loaded and operates; S2, whether a program is required to be updated or not is judged, if yes, the step S3 is executed, and if not, the step S9 is executed; S3, the operating system loads and operates a program updating module; S4, a JTAG downloads a modified application program into a memory; S5, the JTAG writes program information into the predetermined memory; S6, the program updating module writes the application program of the memory into an external storage firmware zone according to program information; S7, a record pointing to the application program is added in a firmware zone file system directory entry; S8, updating completion is prompted, and restarting is performed; S9, a normal application loading state is enabled, and the newest directory entry corresponding to the application is retrieved from the tail to the head of the firmware zone file system directory entry; S10, the application program is loaded through the newest directory entry, operates and is debugged. The invention further provides a device for achieving the method.