The invention discloses a spaceborne high dynamic GNSS receiver and a navigation method thereof. The receiver is based on ARM+FPGA, and comprises a radio frequency front end processing module, a baseband signal digital processing module and a positioning solver module, wherein the radio frequency front end processing module, the baseband signal digital processing module and the positioning solver module are connected in turn. The navigation method comprises the steps that the radio frequency front end processing module carries out amplification, frequency conversion, filtering and analog-to-digital conversion on a satellite signal to acquire a digital intermediate frequency signal; the baseband signal digital processing module carries out capturing, tracking, bit synchronization and frame synchronization on the baseband signal digital processing module to acquire a navigation measurement value and a navigation message; the positioning solver module uses the navigation measurement value and the navigation message to carry out positioning solving; and the satellite information of a user and a positioning observation value are acquired. According to the invention, an ARM+FPGA architecture is used, which is very flexible; different algorithms can be loaded; and an FPGA parallel processing structure can guarantee the timeliness of the GNSS receiver.