The invention discloses a waterstop structure machining device, a method and waterstop structures of an arc-shaped door of a ship lift, and relates to the technical field of mechanical machining devices. The machining device comprises a main shaft which is horizontally erected, and expansion hubs and side machining components are sequentially arranged at the two ends of the main shaft from outside to inside; and a bottom waterstop machining component is arranged at the position, between the two side machining components, of the main shaft. According to the device, the machining period is shortened, the requirement for the coaxiality between two arc-shaped waterstop plates and between two arc-shaped rails is ensured, and the requirement for the radian of a bottom waterstop plate is ensured.