Objective: To analyze the therapeutic effect of modified subdormant therapy combined with ganciclovir on viral encephalitis. Methods: 107 cases of viral encephalitis treated in our hospital from June 2018 to February 2020 were selected for the study, of which 53 patients were treated with ganciclovir and considered as the control group; the other 54 patients were treated with modified suboxone therapy combined with ganciclovir and considered as the study group. The clinical efficacy (total treatment efficiency) and the time to disappear of fever, headache, vomiting and convulsions were compared between the two groups, and the inflammatory response indexes [vascular endothelial growth factor (VEGF), calcitonin gene-related peptide (CGRP), soluble vascular cell adhesion molecule 1 (sVCAM-1) and supersensitive C-reactive protein (hs-CRP)], neurological function indexes [(neuron-specific dilute alcoholase (NSE), matrix metalloproteinase-2 (MMP-2), and central nervous specific protein S100 (S100β)] levels. Results: After treatment, the total treatment efficiency of the study group was higher than that of the control group, and the disappearance of clinical symptoms such as fever, headache, vomiting and convulsions was shorter than that of the control group (P<0.05). After treatment, VEGF, CGRP, sVCAM-1, hs-CRP, NSE, MMP-2 and S100β were lower in the study group than in the control group (P<0.05). Conclusion: Modified subhypophyseal therapy combined with ganciclovir is effective in the treatment of viral encephalitis, which can effectively improve clinical symptoms, reduce inflammatory response and neurological function damage, improve clinical efficacy, and has high clinical application value.