The invention provides a FlexRay bus protocol analysis system and method based on a digital fluorescent oscilloscope. The system comprises a user setting module, a PCIe module, a parameter dwell vessel module, a decoding trigger module, a decoding storage module, a collection module and a display module. According to the system and method of the invention, the speed of hardware decoding is much higher than that of software decoding, hardware carries out decoding while hardware is used to trigger software decoding, decoding information can be stored in the manner of labels on the basis of a triggering scheme determined by software decoding, trigger position information is also stored, superior application software reads stored label information and trigger position information directly for display, a step of software decoding is omitted, the bus analysis speed is improved, and labor cost of secondary decoding by the software is omitted.