Stratification will contribute to the anisotropy of the submarine wave height and a longer and wider influencing zone on the free surface. However, the contribution ratio of appendages to the waveform characteristics on the free surface is unclear. This greatly hindered the research on the optimization design of the submarine shape with the goal of reducing the hydrophysical signatures on the free surface. In this study, taking the Joubert BB2 submarine model as an example, three different types of submarines in the linearly stratified fluid are simulated: a bare hull, a full-appendage Joubert BB2 submarine, and the full-appendage Joubert BB2 submarine with a ducted propeller. The Reynolds number is about 10⁶, and the internal Froude number is about 3 in these three cases. After quantality analyzed the density fluctuations, internal waves, and complex hydrophysical signatures on the free surface of these three cases. The results show that the existence of the appendages will cause an obvious phenomenon on the free surface, and will result in the waveform formed by the submarine on the free surface being “farther”, “wider”, “faster” and longer duration.