Ballast water management is an effective measure to ensure that organisms and bacteria do not migrate with the ballast water to other areas. The International Maritime Organization adopted the International Convention on the Control and Management of Ballast Water and Ship Sediments, in 2004 which regulates issues of ballast water management. Many technologies have been researched and developed; in particular, using UV rays is the method that is evaluated with many advantages and meets the requirements of the Convention. The UV reactor in the ballast water treatment system has a very large capacity, so in the ballast water treatment system, it is often necessary to use many high-power UV lamps in one UV reactor. These high-power UV lamps consume a lot of electrical energy and are very expensive. Research on the control of UV radiation in the process of disinfecting water appropriately and effectively is necessary in order to improve the life of UV lamps, consume less electricity, and ensuring anti-bacterial duty is well conducted. This paper presents the development of a controller for a UV reactor and ballast water flow in the ballast water treatment system installed on ships. Experimental results on ships indicate the efficiency achieved by the developed UV controller.