Background: To investigate the value of pretreatment nasopharyngeal and neck magnetic resonance imaging (NN-MRI) combined with positron emission tomography (PET)/CT-guided therapy for improving survival in upper aerodigestive tract NK/T-cell lymphoma (UADT-NKTL) patients. Methods: We performed a prospective cohort study including 171 untreated patients histologically diagnosed with UADT-NKTL, of whom 71 patients received PET/CT combined with NN-MRI and the other 100 patients received PET/CT alone. The clinical stage of every patient was classified according to the Ann Arbor and TNM staging systems. Clinical stage, target volume delineation, and survival were evaluated and compared for PET/CT with and without NN-MRI. Results: By detecting additional local lesions, NN-MRI upgraded the clinical stages on the basis of the Ann Arbor staging system and TNM staging system compared to the results of PET/CT (9/71, p = 0.011; 11/71, p = 0.019, respectively), which revised the target volume delineation of radiotherapy (9/71) in the PET/CT-MRI group. Compared with those in the PET/CT group, 3-year local recurrence-free survival was prolonged in the PET/CT-MRI group (100% vs. 74.9%; p < 0.001), and 3-year overall survival and progression-free survival were better in the PET/CT-MRI group (84.5% vs. 76.3%, p = 0.04 and 78.3% vs. 67.3%, p = 0.03, respectively). Conclusion: NN-MRI and PET/CT-guided therapy could complementarily assist in optimizing the determination of clinical stage and target delineation, which could improve the prognosis of UADT-NKTL patients.