In order to overcome the low-efficiency and low-accuracy of present manual demarcation method for the sub-bottom layers, an automatic demarcation and extraction method based on sediment quality factor and peak-trough on the echo energy loss level curve was proposed. Firstly, the original SEGY file from sub-bottom profile (SBP) was decoded and the amplitude data of each trace was transformed to echo intensity data, so that original sub-bottom profile image can be obtained. Secondly, aiming at eliminating the impact of abnormal observation data, the trace-repair, de-noising, multiple-elimination were carried out. Thirdly, the sediment quality factor was extracted by spectral ratio method, at the same time, the peaks and troughs were also extracted on the echo energy loss level. Then, the locations corresponding to the sediment quality factor and peak were recorded respectively, which were combined to gain the control peaks by employing weighted average method. On the basis of control peaks, the typical peaks corresponding to the actual layer interfaces were searched out. Finally, considering the gradualness and continuity of the sub-bottom sediment structure, the discrete layer interfaces were connected to continuous sub-bottom layer interfaces by means of the Mode smooth approach. The experimental results show that the relative error of demarcation for sub-bottom layers comparing with the in-situ coring data was about 2%, the proposed method can realize automatic extraction for sub-bottom layers and achieve the same accuracy as coring sample data.