Subarray technology is an effective solution to the “conflict of sum and difference” in a large array radar. However, the optimal subarray partition method is a difficult problem both in the theoretic and practices. By exploring the advantage of genetic algorithm, a method, to optimize the subarray configuration in monopulse application, is proposed in this paper. The innovative method is subtly designed and discussed in-depth. Numerical results are presented to validate the effectiveness of the innovative method.