As an instrument to measure stratigraphic section of water bottom, sub-bottom profiler has been a key tool in harbour construction, navigation engineering and other fields of water transport engineering. To ensure right measuring result and improve project quality, it is badly in need of studying the measurement standard. This paper expounds the measuring error of depth and vertical resolution, and especially gives the method of traceability of value on depth and vertical resolution. It analyzes some questions about establishing measurement standard in the end. The study will fill in the blanks of metrological technology in sub-bottom profiler.