The invention discloses a water bag ballast water system for immersed pipe sinking. A water loading unit comprises a plurality of water bag groups, and the number of the water bag groups is even; a pipeline unit comprises two main water pipelines, a ventilation pipeline and a plurality of branch water pipelines; the two main water pipelines are symmetrically arranged relative to the center line ofthe length direction of the immersed pipe, one end of a water bag group water inlet and outlet pipeline is connected with the main water pipelines, the other end of the water bag group water inlet and outlet pipeline is connected with the water bag groups, and one water bag group water inlet and outlet pipeline is arranged at each water bag group; the two ends of ballast pipelines are connected with the main water pipelines, a drainage pump is installed on each ballast pipeline, and hydraulic valves are installed at outlets of the drainage pumps on the ballast pipelines and the connecting sections of the main water pipelines and the ballast pipelines; the ventilation pipeline is installed on one side of a butt-joint end of the immersed pipe, one end of the ventilation pipeline is connected with an end sealing door, and the other end is suspended. A traditional construction method is replaced, a system which is lower in investment cost and more convenient is adopted, and safe, rapid and stable sinking of the pipe joint is achieved.