In the numerical simulation of welding residual stress (WRS), the thermal fields distribution of the weld beads during welding process is the basic data to calculate the residual stress due to thermal expansion and extraction. Different welding heat input control method had been proposed and used in the WRS finite element method (FEM) analysis, such as input based on theory, input controlled by temperature monitoring point and so on. Some disadvantages like less calculating efficiency, unexpected temperature variation have been found in these methods. Based on the study of the FEM result of temperature distribution through the weld butter field by using constant unit heat input, the heat transfer activities of each weld bead were researched. And a novel heat input fitted equation was proposed to describe the suitable heat input data for each weld bead of the welding process. More reliable and uniform melting temperature of weld beads with different location could be achieved. And the welding residual stresses from different welding thermal field of theory method, temperature monitoring point method, and novel heat input equation method are compared with the measured WRS results. The results show that the WRS achieved from the novel heat input equations is close to the measured result and has more computational efficiency. The uncertain WRS data used for probability safety assessment were also proposed based on the FEM results with the novel heat input equation method.