The invention provides an underwater topography measurement system as well as a manufacturing method and a measurement method. The underwater topography measurement boat is composed of at least one measurement boat, a standard station, main manipulation equipment and remote control equipment, wherein the standard station, the main manipulation equipment and the remote control equipment are implemented and manipulated on the bank; a plurality of measurement boats can be simultaneously manipulated by the standard station, the main manipulation equipment and the remote control equipment; each measurement boat is composed of a boat body, a control system, a navigation direction control system, a positioning system, a measurement system and a communication system; the whole boat body of each measurement boat is independently composed of a boat head and a boat body by sections; the lower end part of an equipment mounting column is fixedly provided with a probe of a depth sounder; a bearing cabin of the boat body is internally provided with a data communication radio station, a GPS (Global Positioning System) radio station, the depth sounder, a storage battery pack, a power supply module and an industrial control computer; an engine is provided with a starting engine; and the starting engine is composed of an igniting device, a shutdown device and a starting and shutdown detection circuit. The underwater topography measurement boat disclosed by the invention has the advantages of scientific design, reasonable structure, simplicity in operation, convenience and flexibility, convenience for installation and detachment and convenience for transportation and transferring, so that the underwater topography measurement boat is adapted to underwater measurement of various different water areas and the automation of the underwater measurement is realized.