An autonomous driving system having dual secure boot is provided. The autonomous driving system includes: a control system, a host, and a baseboard management controller (BMC). The control system includes a microcontroller, a first flash memory, and a second flash memory. The first flash memory stores first embedded-controller firmware and a first application image file. The second flash memory stores second embedded-controller firmware and a second application image file. When the autonomous driving system is turned on, the microcontroller executes a dual secure boot procedure to execute the first embedded-controller firmware or the second embedded-controller firmware. In response to the microcontroller successfully executing the first embedded-controller firmware or the second embedded-controller firmware, the microcontroller authenticates the first application image file or the second application image file. In response to the BMC executing the authenticated first application image file or second application image file, the host executes a boot procedure.