Efficient diagnosis of apple diseases and pests is crucial to the healthy development of the apple industry. However, the existing single-source image-based classification methods have limitations due to the constraints of single-source input image information, resulting in low classification accuracy and poor stability. Therefore, a classification method for apple disease and pest areas based on multi-source image fusion is proposed in this paper. Firstly, RGB images and multispectral images are obtained using drones to construct an apple diseases and pests canopy multi-source image dataset. Secondly, a vegetation index selection method based on saliency attention is proposed, which uses a multi-label ReliefF feature selection algorithm to obtain the importance scores of vegetation indices, enabling the automatic selection of vegetation indices. Finally, an apple disease and pest area multi-label classification model named AMMFNet is constructed, which effectively combines the advantages of RGB and multispectral multi-source images, performs data-level fusion of multi-source image data, and combines channel attention mechanisms to exploit the complementary aspects between multi-source data. The experimental results demonstrated that the proposed AMMFNet achieves a significant subset accuracy of 92.92%, a sample accuracy of 85.43%, and an F1 value of 86.21% on the apple disease and pest multi-source image dataset, representing improvements of 8.93% and 10.9% compared to prediction methods using only RGB or multispectral images. The experimental results also proved that the proposed method can provide technical support for the coarse-grained positioning of diseases and pests in apple orchards and has good application potential in the apple planting industry.