This paper presents an algorithm for the permanent magnet shape optimization of a large scale BLDC(Brushless DC) motor to minimize the cogging torque. A response surface method (RSM) using multiquadric radial basis function is employed to interpolate the objective function in design parameter space. In order to get a reasonable response surface with relatively small number of sampling data points, additional sampling points are added on the basis of design sensitivity analysis computed by using FEM. The algorithm has 2 stages: the first stage is to determine the PM arc angle, and the 2nd stage is to optimize the magnet pole shape. The developed algorithm is applied to a 5MW BLDC motor to get a minimum cogging torque. After 3 iterations with 4 design parameters, the cogging torque is reduced to 13.2% of the initial one.