We study the effects of high magnetic fields on the structure and on the geometry of the crust in neutron stars. We find that the crust geometry is substantially modified by the magnetic field inside the star. We build stationary and axis-symmetric magnetized stellar models by using well-known equations of state to describe the neutron star crust, namely the Skyrme model (Sky) for the inner crust and the Baym, Pethick, and Sutherland (BPS) equation of state for the outer crust. We show that the magnetic field has a dual role, contributing to the crust deformation via the electromagnetic interaction (manifested in this case as the Lorentz force) and by contributing to curvature due to the energy stored in it. We also study a direct consequence of the crust deformation due to the magnetic field: the thermal relaxation time. This quantity, which is of great importance to the thermal evolution of neutron stars is sensitive to the crust properties and, as such, we show that it may be strongly affected by the magnetic field.