A start-up method for USB disk with synchronous flash memory includes steps of: (a) writing test data into a data cache zone of a flash memory according to an initiate read write clock of a flash memory controller; (b) reading the test data to a memory zone of a USB controller; (c) comparing the test data in two memory zones, and recording a comparison result and a phase parameter of read write clock; (d) delaying the initiate read write clock for one-unit delay, and repeating steps (a)˜(d); (e) if the comparison result changes from success to failure, stopping repeat the step (d); (f) selecting the phase parameter of the read write clock that corresponds to one of the comparison results in an interval with multiple continuous successful comparison results to determine a clock phase for accessing the flash memory, and then starting up the USB flash disk. The method is quick and stable.