Cooling subsequent to the extrusion process is a crucial operation in the aluminum extrusion value chain. Non-uniform cooling induces shape distortions, including deflection and twisting, which reduce the product quality. The interplay between the temperature management by water quenching and the effect of the temperature distribution within the section is, therefore, essential to this process. Appropriate modeling, with both physical and numerical methods, can assist with improving temperature control in extrusion plants. In this study, ABAQUS/Standard software is used to make the finite element (FE) model for the cooling process inside a quench box. A rectangular plate and a simple section with two different thicknesses are used to study the effect of non-uniform and asymmetric cooling across the width. Water cooling from the top side and air cooling from the bottom side are implemented as the cooling starts from one end and moves along the length to the other end. Therefore, the shape distortion due to non-uniform and asymmetric cooling in three directions (through the thickness, across the width and along the length) is discussed. This study shows that the profile experiences a twisting-type distortion across the width under non-uniform cooling. The effect of the non-uniformity ratio, the width ratio, the thickness and the width of the section are studied as well. It is shown that the width ratio has a varying effect as it increases, while the other named parameters have an almost consistent effect: when they are increasing the section always twists more or less. The simulated results are found to be in reasonable agreement with experimental evidence.