The invention discloses a method and a system for processing a data packet check error, comprising the following steps: S1, searching a data packet frame head during data transmission; 2, starting preparatory work as soon as the end flag of the frame header is detected; 3, recording that received byte and performing initial CRC verification calculation; 4, aligning the frame header from the back to the front byte as soon as an error is detected in the calculation result of the initial CRC check; 5, searching the end byte of the frame header, and when the end byte of the frame header is not found, recording the error information; 6, carrying out secondary CRC checking calculation once the end byte of the frame head is detected; 7, detecting the calculation result of the secondary CRC verification. The function of not only recording the error event but also submitting the complete error data packet is realized by detecting the error position, recording the error data and analyze the error cause; It is convenient for communication operators to analyze the causes of errors, to count the number and frequency of errors, to know the stable operation of the whole network more quickly and accurately, and to ensure the safety of network communication.