The application discloses a high-speed amphibious vehicle transmission system with double water jet propellers, relating to the amphibious vehicle. The transmission system is connected with the engine, including a clutch, a gearbox assembly, and a vehicle transmission shaft assembly, a marine transmission shaft and a water jet propeller symmetrically arranged on both sides of the transmission assembly. The gearbox assembly includes: housing, primary shaft, primary shaft gear, intermediate shaft gear, input gear, vehicle input / output gear shaft, vehicle and ship synchronizer assembly, transfer gear, first gear teeth, second-fifth gear input gear , 3rd and 4th gear synchronizer assembly, 1-5th gear output gear, 1st and 2nd gear synchronizer assembly, reverse gear output / input gear, 5th gear reverse gear synchronizer assembly, marine input gear, marine intermediate gear and marine output gear. This application adopts a high-power engine matched with two small-power water jet propulsion structures, with strong output power and small space occupation; all transmission parts adopt integrated design, compact structure, light weight, and stable operation.