The invention discloses a buoyant box type water floating gantry crane pipeline sinking construction method. The method comprises steps as follows: step 1, long steel pipes are welded ashore and lifted onto a controllable buoyant box on the water surface; step 2, all small sections of steel pipes floated by the controllable buoyant box on the water surface are welded into a large section of steelpipe; step 3, a gantry crane lifts steel pipes with inclined pipe sections to be welded with the large section of steel pipe; step 4, a hydrostatic test of the steel pipes is conducted after the wholesection is mounted; step 5, the controllable buoyant box is reversely buckled on the steel pipes, and water is injected into two ends of the steel pipes to make the steel pipes to gradually sink; step 6, after the steel pipes sink, the controllable buoyant box is dismounted, the dismounted controllable buoyant box is inflated to automatically float on the water surface, and trenches are backfilled. Interface butt welding, water surface transportation, pipeline pressure test, sinking and other procedures of pipelines spanning long-distance water channels can be realized. The construction principle is simple and easy to implement, construction machinery such as a large crane is not required, the sinking positions are accurate, and the method is low in cost, safe and reliable.