Automatic pavement disease detection aims to address the inefficiency in practical detection. However, traditional methods heavily rely on low-level image analysis, handcrafted features, and classical classifiers, leading to limited effectiveness and poor generalization in complex scenarios. Although significant progress has been made with deep learning methods, challenges persist in handling high-resolution images and diverse disease types. Therefore, this paper proposes a novel approach based on the lightweight Transformer Patch Labeling Network (LTPLN) to enhance the efficiency of automatic pavement disease detection and overcome the limitations of existing methods. Firstly, the input images undergo histogram equalization preprocessing to enhance image quality. Subsequently, the images are evenly partitioned into small patch blocks, serving as inputs to the enhanced Transformer model. This enhancement strategy involves integrating feature map labels at each layer of the model to reduce computational complexity and enhance model lightweightness. Furthermore, a depthwise separable convolution module is introduced into the Transformer architecture to introduce convolutional bias and reduce the model’s dependence on large amounts of data. Finally, an iterative training process utilizing the label distillation strategy based on expectation maximization is employed to update the labels of patch blocks and roughly locate the positions of pavement diseases under weak supervision. Experimental results demonstrate that compared to the baseline model, the proposed enhanced model achieves a reduction of 2.5G Flops computational complexity and a 16% speed improvement on a private pavement disease dataset, with only a 1.2 percentage point decrease in AUC accuracy. Moreover, compared to other mainstream image classification models, this model exhibits more balanced performance on a public dataset, with improved accuracy and speed that better align with the practical requirements of pavement inspection. These findings highlight the significant performance advantages of the LTPLN model in automatic pavement disease detection tasks, making it more efficiently applicable in real-world scenarios.