As an important physical property of seafloor sediments, the seafloor micro-topography roughness is of great significance to marine engineering and scientific investigation. How to measure seafloor micro-topography roughness by optical method has been a hot topic in this field in recent years. Based on the shape from shading (SFS) algorithm in optics, a fast seafloor micro-topography roughness algorithm was put forward. While constructing the model, the absorption and attenuation model of underwater light propagation was considered, and the seafloor micro-topography roughness was measured and the parameters were fitted according to the power law form. Simulation results prove that the algorithm has 95% confidence, it is suitable for seafloor micro-topography roughness measurement, and its validity and correctness are proved by experiments.