The power transmission system has always been considered critical for a human powered boat(or water bike) since it first showed up at Human Powered Vessel Festival. Mechanical problems, such as abrasions and other damages of the gear system for the power transmission, lead to poor durability and low efficiency of a boat. This paper described mechanical problems and a design process of power transmission system and then suggested the method to solve the problems. It is selected a module and a type of gears that are structurally stable thus can transmit the power durable. Especially the lower gear box is applied to CRP(contra rotating propeller) system for improving the structural stability and the propeller efficiency as well. As the results, the upper and lower gear box are designed and manufactured. And from the trial test, it is confirmed that the power transmission system is reliable.