A novel one-pot synthesis of 2,4-substituted 5-azolylthiopyrimidines is achieved by sequential Michael-addition of 3-iodochromones with mercaptoazole (or mercaptotriazoles) and then condensation with a variety of amidines. Compound A1B6C1 exhibits a potent anti-influenza virus A activity with an IC50 value of 21.56 mg/mL and SI value of 9.