In this paper, the three-dimensional calculation model of 1/72 LSII submarine is established by finite volume method, and combining frame motion, user-defined function and polynomial profile, the simulation of propeller rotation and temperature-density stratified seawater are realized. Based on this model, the effects of diving depth, sailing speed and wake velocity on cold-thermal wake characteristics are analyzed. The conclusions are as follows. 1) Considering the temperature-density stratified seawater is a sufficient and necessary condition for simulating the cold-thermal wake characteristics of submarine. 2) Submarine perturbs the low-temperature seawater to form the cold wake, then the cold wake and the thermal wake are superimposed to form the cold-thermal wake characteristics in downstream sea-surface. 3) Cold wake characteristics of upstream sea-surface are related to the diving depth directly, but aren’t related to the sailing speed and wake velocity. The contents above could provide reference for the high-precision simulation of submarine’s cold-thermal wake characteristics.