This paper concerns high-power laser welding of thick plates for the ship industry. Thermomechanical behavior during laser welding of 16 mm marine steel EH40 using 25 kW laser power was investigated by a 3D finite elements model. The objective is to analysis the effects of weld collapse and hump on the residual stress induced thermal cycle. A double-cylindrical source model was proposed to simulate the transient distribution of temperature field. Heat flow distribution area is a cylinder, radial heat flow presents a Gaussian distribution, while heat flow peak in the direction of thickness is decaying then increasing exponentially. The predicted weld geometry had good agreement with the actual results. When collapse and hump were considered, simulation error of temperature distribution was reduced from 10.85–1.54%. In addition, cooling curves obtained from the thermal simulation were incorporated into the continuous cooling transformation diagram of EH40 to explain the evolution mechanism of microstructure. It was shown that collapse and hump affected the values and distribution trend of residual stress in different thickness, especially in the high gradient stress zone near the weld center.