In this paper, the uncertainty analysis method of ITTC (2017) for ship model self-propulsion tests was studied, and the defects of the ITTC method were analyzed, which didn’t provide the method to analyze the tests results at different temperatures. Combined with the ship model self-propulsion tests carried out by SSSRI, an improved uncertainty analysis method was proposed. First of all, the ship model self-propulsion test process was combed to determine the error sources of uncertainty, and then according to the test principle of self-propulsion tests, an conversion method of test data at different temperatures was put forward. Furthermore, this improved method can be an additional procedure of ITTC on the uncertainty analysis of self-propulsion tests. At the same time, the steps and methods of uncertainty analysis of ship model self-propulsion tests can be used as a reference for other towing tank tests. At last, an example of the uncertainty analysis of self-propulsion results in SSSRI was presented. The results show that at the nominal temperature of 15°C, at 95% confidence level, the expanded uncertainty of rotational speed n is less than 0.4%, and the expanded uncertainty of thrust T and torque Q is less than 1.0%. The expanded uncertainty of thrust deduction factor t is less than 5.5%, wake fraction w 1.1%, which shows that the test in this paper has achieved high accuracy.