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 element model. The objective is to analyze 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 only 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. The collapse mainly affects the residual stress distribution on the top surface, while the hump affects that on the bottom surface. Both of them have little influence on the residual stress in the middle thickness area. The cold contraction of weld metal and the stress concentration caused by weld shape during the cooling process are the fundamental reasons that collapse and hump affect the distribution of welding residual stress.