Diplodia tip blight caused by Sphaeropsis sapinea (Fr.) Dyko and B. Sutton is a serious threat to the health of natural secondary Japanese red pine (Pinus densiflora Sieb. et Zucc.) forests. To explore the effect of plant diversity on Diplodia tip blight disease occurrence, the correlation between Diplodia tip blight in P. densiflora and plant diversity in various stand types and vertical structure layers were analyzed by Pearson correlation coefficients and generalized linear model while keeping environmental factors relatively consistent. Disease index of Diplodia tip blight in P. densiflora was positively correlated with the plant diversity indices in the tree layers of P. densiflora–conifer mixed forest. In contrast, it was negatively correlated with the plant diversity indices in the tree layers of P. densiflora–hardwood mixed forest and P. densiflora pure forest. In shrub–herb layers of all stands except the P. densiflora pure forest herb layer, the disease index was positively correlated with the plant diversity indices. The prediction models for the disease index of Diplodia tip blight in the P. densiflora–hardwood mixed forest, P. densiflora–conifer mixed forest, and P. densiflora pure forest were also established. The foregoing results suggest that in the Kunyu Mountains of China, the differences in plant diversity among various stand types and vertical structure layers have different effects on the occurrence of Diplodia tip blight in P. densiflora. Plant diversity largely reflects the occurrence of Diplodia tip blight disease. However, if the effect of plant diversity on Diplodia tip blight is fully reflected, the plant species characteristics, especially tree genetic relationships, should be considered. In this way, plant species diversity structure in natural secondary Japanese red pine forests may be modified through forest management to lower the incidence of Diplodia tip blight.