The three-dimensional model of 1/72 LSII nuclear submarine was established using the finite volume method, and the simulation of high-speed rotating propeller and temperature-density stratified seawater were realized combining the frame motion, user defined functions and physical polynomial profile. Based on this model, the influences of factors such as high-speed rotating propeller, temperature-density stratified seawater and high-temperature thermal spray on the heat and mass transfer characteristics of submarine cold-thermal wake were discussed. The results indicate that high-speed rotating propeller induces the increase of backward delay distance of thermal wake and the decreases of sea surface temperature difference. Ignoring the rotation, absolute error and relative error of sea surface temperature difference is 3.23 mK and 52.7% respectively. Cold wake signal is formed by the rise of temperature-density stratified seawater which is disturbed by underwater navigation submarine. Compared with temperature-density uniform seawater, temperature-change area increases significantly and wake temperature difference rises from 6.13 mK to 84 mK. Existence of underwater navigation submarine can be judged by the cold wake characteristics in the upstream sea surface; if submarine exists, its position can be inversed precisely combining the thermal wake characteristics in the downstream sea surface. The above results can provide reference for optimizing the simulation accuracy of submarine cold-thermal wake.