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A series of novel 3-phenoxy-4-(3-trifluoromethylphenyl)pyridazines <b>2</b>–<b>5</b> were designed, based on the structure of our previous lead compound <b>1</b> through the in silico structure-guided optimization approach. The results showed that some of these new compounds showed a good herbicidal activity at the rate of 750 g ai/ha by both pre- and post-emergence applications, especially compound <b>2a</b>, which displayed a comparable pre-emergence herbicidal activity to diflufenican at 300–750 g ai/ha, and a higher post-emergence herbicidal activity than diflufenican at the rates of 300–750 g ai/ha. Additionally, <b>2a</b> was safe to wheat by both pre- and post-emergence applications at 300 g ai/ha, showing the compound’s potential for weed control in wheat fields. Our molecular simulation studies revealed the important factors involved in the interaction between <b>2a</b> and <i>Synechococcus</i> PDS. This work provided a lead compound for weed control in wheat fields.