An effective method is proposed to suppress the second-order beams(SOBs) that result from the cross-polarized fields of 2D edge slot arrays. By rearranging the conventional sequence of stacking waveguides, the SOBs are shown to be considerably reduced and the 9 dB suppression is obtained. The optimal sequence is obtained from the genetic and exhaustive searches and its effects are verified using near-field measurements as well as theoretical estimation. Since the proposed method requires no additional polarizing structures such as baffles, it is very easy and cost-effective to implement.