With the aim of exploring new benzimidazole derivative with high fungicidal activity, a series of novel 2-(2-(alkylthio)-6-phenylpyrimidin-4-yl)-1H-benzimidazoles were designed and synthesized, and their in vitro fungicidal activities were evaluated. Compounds 5a, 5f, 5g, 5h, 5i and 5l exhibited excellent fungicidal activities against Botrytis cinerea, and 5c, 5f, 5h, 5i and 5l displayed notable fungicidal activities against Sclerotinia sclerotiorum. Among them, compound 5i (R<sup>1</sup> = fluorine, R<sup>2</sup> = benzyl) displayed the best activity towards the two tested fungi. Docking study of 5i with β-tubulin protein revealed that the NH moiety of benzimidazole ring generated a hydrogen bond with Gln-11 residue, and the fluorine atom of benzene ring formed a hydrogen bond with Tyr-208 residue, respectively; the benzene ring of Tyr-222 and the pyrimidine ring of 5i yielded a π-π interaction. The molecular electrostatic potential analysis elucidated the nitrogen atom of benzimidazole ring, fluorine atom of benzene ring and sulfur atom of thioether moiety were located in the negative potential regions, whereas some hydrogen atoms of benzene, benzimidazole and pyrimidine rings were located in the positive potential regions. This analysis demonstrated the reason why 5i can form hydrogen bonds with amino acid residues of target protein.