Background: To evaluate computed tomography (CT) and magnetic resonance imaging (MRI) fusion images for delineating gross tumor volume (GTV) in three-dimensional conformal radiotherapy (3D-CRT) of nasophanrygeal carcinoma (NPC), and compare treatment outcomes between CT- and CT+MRI-based targets. Materials and Methods: A total of 120 NPC patients treated with 3D-CRT were included, in which, 60 each were treated with CT-based and 60 with CT+MRI fusion targets. We explored the clinical application of CT+MRI fusion targets and compared the 1-, 3-, and 5-year survival and relapse rates between both targets. Results: The clinical characteristics and treatment factors were well balanced. The differences in public volume using CT alone in the CT+MRI (Group A) and the CT arm (Group B) were not significant (33.6±2.18 vs. 34.3±2.98, P > 0.05). The public volumes of GTV in the two arms were 49.48±2.46 cm³ and 33.6±2.18 cm³ respectively (P < 0.05). CT+MR fusion images did not influence the one-, three-, and 5-year survival rates (100% vs. 98.3%, 85.0% vs. 81.2%, and 73.3% vs. 68.3%, respectively). The three- and 5-year out-of-field progression was reduced in the CT+MRI arm. However, only the difference in 3-year out-of-field relapse rate was significant (3.3% vs. 13.3%; P < 0.05). The incidence of acute toxicities was similar between groups. Conclusion: The variability in GTV delineation in NPC was ascribed to intermodality and not interobserver variability. CT+MR fusion images likely reduced the 3-year out-of-field relapse rate.