Cervical intraepithelial neoplasia is the primary type of cervical precancerous lesion; however, manual clinical diagnosis is prone to bias and has limited grading accuracy. To achieve precise automated grading of CIN, this paper proposes a multimodal fusion Swin Transformer model and develops a corresponding computer-aided diagnosis system. This method employs three-channel fusion of raw images, cervical mask images, and directional gradient histogram features to enhance lesion texture and location information. Within the Swin Transformer backbone, an atrous spatial pyramid pooling module channel attention module and a convolutional feature extraction module are embedded to balance global semantic and local detail features. A focal loss function is adopted to address class imbalance in the dataset and improve the model’s ability to identify difficult-to-classify samples. On a dataset of 3 915 clinical colposcopy images, the model achieved an overall accuracy of 90.01%, precision of 87.55%, recall of 86.17%, F1 score of 89.13%, outperforming baseline models such as VGG, ResNet, and Swin Transformer. The developed system integrates image quality screening, lesion identification, and three-level classification functions, providing an effective tool for the rapid and objective screening of clinical cervical precancerous lesions.