To make up for the deficiencies of existing sounding method in obtaining the seabed microtopography, a linear algorithm to obtain three-dimensional sea topography using side scan sonar image based on its high resolution features is proposed. Firstly, the incident sound direction estimation model is given according to the side scan sonar imaging mechanism, and the linear inversion algorithm is derived from the seabed lambert model. Meanwhile, the constraint model is built using the initial terrain data of the same area, and the transform from inversion topography to real topography is completed. Based on the above, the inversion process and the accuracy evaluation method are finally achieved. Lastly, experiments are carried out to test and verify the given method. Experimental results show that this method can obtain the topography whose accuracy is better than 15 cm and whose resolution is about 170 times higher than that of the initial terrain.