In this paper, a novel laser scanning system for deep sea in-situ measurement was developed. Firstly, the main components of the prototype were introduced separately. Then, the performance of the system was tested and analyzed in a tank filled with water with a standard ball bar. Results showed that the laser scanning system in water can achieve high precision. In addition, the prototype was placed in deep sea to verify the performance of the in-situ measurement. The measured targets are well reconstructed, as well as the high precision of underwater in-situ measurement was obtained.