Abstract: The temperature rise of the material during the fatigue process is mainly caused by energy dissipation, which can be used to evaluate the fatigue performance of materials or components. However, changes in the thermal boundary conditions during the test is likely to make the evaluation result unreliable. In this paper, the fatigue performance of AZ31B magnesium alloy manual TIG welded joint was evaluated by using the temperature rise caused by energy dissipation. In order to overcome the adverse effects of changes in boundary conditions, based on the superposition principle of boundary value problem of linear partial differential equation, this paper proposes to divide the raw temperature data measured by infrared camera into two parts: temperature rise caused by boundary conditions and temperature rise caused by energy dissipation. On this basis, it is further proposed that the temperature rise caused by energy dissipation can be used to evaluate fatigue performance. Moreover, a temperature data processing method was given according to the proposed theory. The results showed that, based on the processed temperature data, the fatigue limit of the ground flush joint and the as-welded joint are 58.85 and 62.61 MPa respectively by the classical energy dissipation method (Risitano method), whose errors relative to the fatigue limit obtained by the S-N curve (2 × 10⁶) are −11.82% and −0.03%, respectively.