In order to solve the problems in the monitoring of algae concentration, such as the traditional fixed-point monitoring method covers a small area, the remote sensing monitoring method has a large error, the processing algorithm is complicated, in addition, the vertical distribution and change pattern of algae concentration cannot be obtained, the threedimensional monitoring system of algae concentration based on the unmanned ship is designed. First, design a longendurance unmanned ship with fuel-powered, and onshore terminal can control it to reach the designated measurement position; Second, the unmanned ship carries the submersible, and the shore side can control the ascent and descent of the submersible, as well as the acquisition and transmission of sensor data. Combined with satellite positioning data to display real-time the navigation video of the unmanned ship, various sensing data such as measured data of algae concentration, water depth pressure and so on, to complete the three-dimensional monitoring of algae concentration. Finally, tests were carried out in the sea near Tielu Port, Sanya, through the measurement of 144 locations at 9 stations, it was found that the vertical distribution of algae had phototaxis, showing that its concentration gradually decreases from the surface to the depths of the ocean.