Abstract: In sub-bottom profile data processing, the artificial picking method is inefficient and can be influenced by human factors significantly, and the semi-automatic picking method needs the human intervention and the accuracy is low. In order to solve these problems, this paper proposes a method of using gray scale mutation and constraint of horizon direction to pick sub-bottom horizon automatically. Firstly, a pre-pick method based on gray scale mutation is used. Secondly, based on the continuity principle, a method of horizon tracking and filtering is proposed, which realizes the connecting of discrete horizon and filtering out of the irregular horizons. And then, taking the correlation of the ping sequence and horizon direction into consideration, a horizon growth method based on the direction constraint is proposed to realize the connectivity of discontinuous horizon. Finally, the process of horizon picking is given, and the results are verified by experiment.