To obtain the optimal water spray velocities of on-line quenching system, a finite element model for simulating the on-line quenching process of large section π-shaped aluminum profiles was established based on Fluent and Workbench software platform. To determine the thermal boundary conditions in the simulation, methods in spray quenching experiments combined with inverse heat conduction were used to get the heat transfer coefficients under different spray water fluxes. The velocity, temperature, stress fields and residual deformation of extruded profiles during on-line quenching process under three schemes with different nozzles velocities were analyzed systematically. The results show that the heat transfer coefficient increases with the increase of spray water flux, and the time to reach the peak value is later. The simulated temperatures of feature points present corresponding changes with the measured ones and the relative error range is -0.7~7.8%, which verifies the accuracy of finite element model. For the initial quenching process scheme, a large thermal stress is formed at the joint position due to the non-uniform cooling of profile section, which leads to concave defect at the upper surface of profile. A relatively uniform temperature field can be obtained on the surface and middle section of profile by adopting the scheme 3, and the minimum residual stress and deformation can be achieved. The research methods and results are helpful to the design of nozzles velocities in the on-line quenching system for hollow aluminum profiles extrusion.