The invention belongs to an embedded system file processing method. The invention particularly relates to a Hex file processing method and application. The method comprises the following steps: step 1, grouping Blocks of a Hex file, each group comprising at least one Block, performing CRC check on a specified address field of each group of Blocks to obtain a corresponding CRC check code, and putting the CRC check code into a specified address position, namely a CRC placement address, according to an Intel format; wherein the specified address field does not contain a CRC placement address; step 2, encrypting a data domain in each Record, and setting a corresponding decryption program in a controller pre-flashed by the Hex file; step 3, recalculating the checksum of each encrypted Record; step 4, flashing the processed Hex file into the pre-flashed controller, and decrypting the pre-flashed controller through a decryption program; and step 5, accounting the CRC check code by the pre-flashed controller. By means of the Hex file processing method, the problem that in the prior art, a file in the Hex format is directly used for program flashing, and a program is prone to being crackedor rewritten due to data outflow is solved.