A series of novel N‐(substituted phenyl/benzyl)‐2‐methylthio‐4‐((pyridin‐3‐ylmethyl)amino)pyrimidine‐5‐carboxamides were synthesized by multistep reactions. The structures of the target compounds were characterized by IR, 1H NMR, 13C NMR, and elemental analysis. Their in vitro antifungal activities against two kinds of plant pathogenic fungi were evaluated by the mycelial growth rate method. The result showed that at the dosage of 100 μg/mL, several of these compounds exhibited moderate activity against Botrytis cinerea with inhibition rates of ~70%, and most compounds (e.g., 5a, 5c, 5e, 5f, and 5h) possessed excellent activity against Sclerotinia Sclerotiorum with more than 90% inhibition rate.