Efficient, rapid, and non-destructive detection of pesticide residues in fruits and vegetables is essential for food safety. The visible/near infrared (VNIR) and short-wave infrared (SWIR) hyperspectral imaging (HSI) systems were used to detect different types of pesticide residues on the surface of Hami melon. Taking four pesticides commonly used in Hami melon as the object, the effectiveness of single-band spectral range and information fusion in the classification of different pesticides was compared. The results showed that the classification effect of pesticide residues was better by using the spectral range after information fusion. Then, a custom multi-branch one-dimensional convolutional neural network (1D-CNN) model with the attention mechanism was proposed and compared with the traditional machine learning classification model K-nearest neighbor (KNN) algorithm and random forest (RF). The traditional machine learning classification model accuracy of both models was over 80.00%. However, the classification results using the proposed 1D-CNN were more satisfactory. After the full spectrum data was fused, it was input into the 1D-CNN model, and its accuracy, precision, recall, and F1-score value were 94.00%, 94.06%, 94.00%, and 0.9396, respectively. This study showed that both VNIR and SWIR hyperspectral imaging combined with a classification model could non-destructively detect different pesticide residues on the surface of Hami melon. The classification result using the SWIR spectrum was better than that using the VNIR spectrum, and the classification result using the information fusion spectrum was better than that using SWIR. This study can provide a valuable reference for the non-destructive detection of pesticide residues on the surface of other large, thick-skinned fruits.