Alternaria alternata (A.alternata) is a major pathogenic fungus that causes black mold disease in pears, goji berries, and other crops. In this study, we investigated the inactivation mechanism and kinetics of A.alternata by using contact glow discharge plasma (CGDP). First, the optimal sterilization process and conditions were determined by examining the effects of exposure time, electrolytes, and voltage on the fungicidal rate. Second, the sterilization mechanism of A.alternata by CGDP was studied by evaluating cell membrane integrity and leakage of spore nucleic acids and proteins, and an inactivation kinetic model was constructed. These results showed that CGDP had a significant sterilization effect on A.alternata.. The sterilization rate increased with increasing voltage and treatment duration. Leakage of spore nucleic acids and proteins gradually increased with increasing treatment time. Propidium iodide and Fluorescein diacetate staining, as well as scanning electron microscopy indicated that the effect of CGDP on A.alternata was due to the disruption of its morphology and cell membrane integrity. Spore inactivation kinetics were consistent with dose-response modeling, and the results provide an important theoretical basis for further studies on the bactericidal mechanism of A.alternata.