Black spot disease, caused by Alternaria alternata, is a major microbial disease that apples are highly susceptible to during storage and transportation. In this study, the effect of 0.1 mmol L−1 sodium nitroprusside, a nitric oxide (NO) donor, in controlling black spot disease was evaluated. The results revealed that NO effectively decreased lesion diameter and reduced the accumulation of Alternaria toxins. The possible mechanism of NO-induced resistance against A. alternata is related to key metabolic enzymes of phenylpropanoid metabolism and pathogenesis-related proteins. Moreover, the production and accumulation of resistance-related substances had positive effects. Above all, this study explored possible mechanisms about NO improving apple resistance to black spot disease.