The invention discloses a flexible waterproof device for the joint of an anchor rod and a bottom plate and a construction method of the flexible waterproof device. The flexible waterproof device comprises a waterproof layer and a shell water stop steel plate. The waterproof layer is arranged on the outer side of the shell water stop steel plate. The anti-floating anchor rod penetrates the center position of the waterproof layer and the center position of the shell water stop steel plate, and the root of the anti-floating anchor rod and bottom plate steel bars in the bottom plate are bound andfixed. The appearance of the shell water stop steel plate is hemispheric, and a spherical shell of the shell water stop steel plate is filled with polyurethane. According to the flexible waterproof device and the construction method thereof, the structure is reasonable; the shell water stop steel plate is arranged to stop permeation of pressure water so as to cover the shortage that the anchor rodpenetrates the waterproof layer to weaken the waterproof capacity, and the waterproof effect is enhanced; the waterproof layer, the shell water stop steel plate and the polyurethane form three waterproof measures, the waterproof effect is guaranteed, and the problem that water permeation is prone to happening to the joint of the anchor rod and the bottom plate is effectively solved; and accordingto the construction method, construction is simple and convenient, operation is easy, and good effects are achieved for guaranteeing construction quality and saving construction cost.