Free-space optical communication (FSO) has attracted more and more attention because of its advantages of high-speed, convenience and strong ability of anti-electromagnetic interference, and has become a research hotspot in military and civilian fields. A method of 3D ship deformation measurement is proposed. A time unit is designed by FSO technology. The optical structure of system can realize the measurement of 3D ship deformation angle, the stimulation of optical imaging of receiving unit and the timing of measurement results at the same time. The structure of the system and the design of key circuit are represented. The system error is analyzed with data simulation. The results indicate that this measurement method is theoretically feasible, and not only meets the measurement precision, but also has lower hardware complexity and higher availability. It is potential to be used in practice.