A numerical method to solve a constrained optimal control problem governed by a generalized Ginzburg-Landau model which describes the phase transitions taking place in the superconducting thin films with variable thickness. The method is based on a finite element method to approximate the state equations and an exterior penalty function algorithm to solve the discrete optimal control problem. The convergence of the discrete optimal solutions to the continuous optimal solutions and the convergence of the exterior penalty function algorithm are proved. The objective of the work is to study efficient numerical methods for exploring the possibilities of controlling the motion of vortices in the superconducting thin films through the external magnetic field.