Botrytis cinerea cause postharvest diseases on fruit and lead economic losses. Application of environment-friendly natural compounds is an alternative for synthetic fungicides to control postharvest disease. Lycorine is an indolizidine alkaloid which is widely used for human drug design, however, application of lycorine in controlling postharvest disease and the underlying mechanisms have not been reported. In this study, the effects of lycorine on mycelium growth, spore germination, disease development in apple fruit, cell viability, cell membrane integrity, cell wall deposition, and expression of mitogen-activated protein kinase (MAPK) and GTPase of B. cinerea were investigated. Our results showed that lycorine was effective in controlling postharvest gray mold caused by B. cinerea on apple fruit. In the in vitro tests, lycorine strongly inhibited spore germination and mycelium spreading in culture medium. Investigation via fluorescein diacetate and propidium iodide staining suggested that lycorine could damage the membrane integrity and impair cell viability of B. cinerea. Furthermore, the expression levels of several MAPK and GTPase coding genes were reduced upon the lycorine treatment. Taken together, lycorine is an effective and promising way to control postharvest disease caused by B. cinerea.