The invention relates to a ship lock double-layer water conveying system with a longitudinally-through drainage type lock bottom. The ship lock double-layer water conveying system comprises a ship lock chamber, a first diversion port, a middle branch gallery, a second diversion port, water conveying main galleries located on two sides of the ship lock chamber, filling valves arranged on the upstream portions of the water conveying main galleries, and drain valves arranged on the downstream portions of the water conveying main galleries; the water conveying main galleries communicate with an inlet of the first diversion port through T-shaped pipes, and an outlet of the first diversion port communicates with the second diversion port through the middle branch gallery; the second diversion port communicates with the third diversion port located in the upper layer through a vertical shaft, the third diversion port communicates with a water drainage branch gallery, and the water drainage branch gallery communicates with water drainage holes, and energy dissipation cover plates are arranged on the water drainage holes; and the elevations of the first diversion port, the middle branch gallery and the second diversion port are consistent with those of the drain valves, and the third diversion port, the water drainage branch gallery, the water drainage holes and the energy dissipation cover plates are located on the elevation surface of a lock chamber bottom plate. According to the ship lock double-layer water conveying system, the pressure characteristics of the diversion ports canbe improved to avoid cavitation and cavitation erosion, moreover, outflow can be dispersed to the maximum extent, and the water conveying safety and the water conveying efficiency of the ship lock are improved.