5059 aluminum alloy has become the preferred choice for the ship structure due to its excellent mechanical properties and corrosion resistance. However, the current code lacks the S-N fatigue curve of the 5059 aluminum alloy, imposing difficulties on the fatigue evaluation of the 5059 aluminum alloy ship structure. The 5059 aluminum alloy and a typical marine welded joint are designed to carry out the fatigue tests at the room temperature and the low temperature (-35℃). The corresponding fatigue S-N curve is fitted by the least square method based on the test data. A finite element model of the specimen for fatigue test is established, and the stress obtained by the finite element analysis is extrapolated to obtain the hot spot stress. The fatigue life of the fatigue specimen is predicted by using the fitted S-N curve and compared with the result from the fatigue test. The results show that the proposed S-N curve of the 5059 aluminum alloy material and the welded joint can be used to predict the fatigue life of the ship structure under the low temperature environment.