Accurate apple origin identification and non-destructive internal quality evaluation are important for fruit traceability, quality grading, and post-harvest management. Unlike previous studies mainly focusing on origin classification, this study established a dual-task near-infrared spectroscopy framework integrating geographical origin classification and soluble solid content (SSC, °Brix) prediction for Fuji apples. Samples were collected from three representative production regions in China: Alar in Xinjiang, Yantai in Shandong, and Luochuan in Shaanxi. Near-infrared diffuse reflectance spectra were acquired from 375 apples, generating 3000 spectral samples for origin classification and 750 SSC-calibrated samples for sugar content prediction. For classification, six deep learning models were evaluated using standardized full-spectrum input without chemometric spectral preprocessing, and the Transformer achieved the best performance, with a test accuracy of 96.22%. For SSC regression, spectra were preprocessed using standard normal variate and Savitzky–Golay filtering. The DNN model achieved the best prediction performance, with MAE = 0.5958 °Brix, RMSE = 0.7333 °Brix, R² = 0.8646, and Pearson r = 0.9338. These results indicate that near-infrared spectroscopy combined with deep learning can support both Fuji apple origin authentication and non-destructive local tissue SSC assessment.