The diagnosis of cervical lymph node metastasis from thyroid cancer is an essential stage in the progression of thyroid cancer. The metastasis of cervical lymph nodes directly affects the prognosis and survival rate of patients. Therefore, timely and early diagnosis is crucial for effective treatment and can significantly improve patients’ survival rate and quality of life. Traditional diagnostic methods, such as ultrasonography and radionuclide scanning, have limitations, such as complex operations and high missed diagnosis rates. Raman spectroscopy and FTIR spectroscopy can well reflect the molecular information of samples, have characteristics such as sensitivity and specificity, and are simple to operate. They have been widely used in clinical research in recent years. With the development of intelligent medical diagnosis technology, medical data shows a multi-modal trend. Compared with single-modal data, multi-modal data fusion can achieve complementary information, provide more comprehensive and valuable diagnostic information, significantly enhance the richness of data features, and improve the modeling effect of the model, helping to achieve better results. Accurate disease diagnosis. Existing research mostly uses cascade processing, ignoring the important correlations between multi-modal data, and at the same time not making full use of the intra-modal relationships that are also beneficial to prediction. We developed a new multi-modal separation cross-fusion network (MSCNet) based on deep learning technology. This network fully captures the complementary information between and within modalities through the feature separation module and feature cross-fusion module and effectively integrates Raman spectrum and FTIR spectrum data to diagnose thyroid cancer cervical lymph node metastasis accurately. The test results on the serum vibrational spectrum data set of 99 cases of cervical lymph node metastasis showed that the accuracy and AUC of a single Raman spectrum reached 63.63% and 63.78% respectively, and the accuracy and AUC of a single FTIR spectrum reached 95.84% respectively and 96%. The accuracy and AUC of Raman spectroscopy combined with FTIR spectroscopy reached 97.95% and 98% respectively, which is better than existing diagnostic technology. The omics correlation verification obtained correlation pairs of 5 Raman frequency shifts and 84 infrared spectral bands. This study provides new ideas and methods for the early diagnosis of cervical lymph node metastasis of thyroid cancer.