A novel bis-heterocyclic compound was synthesized and characterized. The crystal structure of the title compound (C22H20ClN5OS, Mr = 437.94) has been determined by single-crystal X-ray diffraction. The crystal is of triclinic, space group P-1 with a = 8.646 (2), b = 9.148 (3), c = 14.540 (4) Å, α = 94.422 (4), β = 98.500 (4), γ = 102.823 (4)°, V = 1101.8 (5) Å3, Z = 2, F(000) = 312, Dc = 1.320 g/cm3, μ = 0.2900 mm−1, the final R1 = 0.041000 and wR2 = 0.1160 for 2675 observed reflections with I > 2σ(I). A total of 5623 reflections were collected, of which 3866 were independent (Rint = 0.019000). The fungicidal activity of title compound was determined, the results showed the title compound displayed moderate fungicidal activity against G. zeae Petch, Phytophthora infestans (Mont.) de Bary, Botryosphaeria berengeriana f. sp. piricola (Nose) koganezawa et Sakuma, Fusarium oxysporum f.sp. cucumerinum, and Cercospora arachidicola.