Ni(II) complexes with N-2-fluorobenzoylpiperidine-1-carbothioimidate (L2-), N-4-fluorobenzoylpiperidine-1-carbothioimidate (L3-), N-2-fluorobenzoylmorpholine- 1-carbothioimidate (L5-) and N-4-fluorobenzoylmorpholine-1-carbothioimidate (L6-) have been synthesized and characterized by elemental analysis, FTIR and 1H-NMR. The crystal structures of three ligands (HL2, HL3 and HL6) and the corresponding Ni(II) complexes ([Ni(L2)2], [Ni(L3)2] and [Ni(L6)2]) have been determined by X-ray diffraction. The antifungal activities of the Ni(II) complexes together and the corresponding ligands against the fungi Botrytis cinerea, Trichoderma spp., Myrothecium and Verticillium spp. have been investigated. The experimental results showed that the ligands and their complexes have antifungal abilities. When the fluorine was substituted on the para-benzoyl moiety, the antifungal activity of the ligands was obviously increased. Moreover, the ligands were stronger than their complexes in inhibiting fungal activities. The antifungal ability of HL6 is especially strong, and similar to that of the commercial fungicide fluconazole.