Objective. Its goal was to see how convolutional neural network- (CNN-) based superresolution (SR) technology magnetic resonance imaging- (MRI-) assisted transition care (TC) affected the prognosis of children with severe viral encephalitis (SVE) and how effective it was. Methods. 90 SVE children were selected as the research objects and divided into control group (39 cases receiving conventional nursing intervention) and observation group (51 cases performed with conventional nursing intervention and TC intervention) according to their nursing purpose. Based on SR-CNN-optimized MRI images, diagnosis was implemented. Life treatment and sequelae in two groups were compared. Results. After the processing by CNN algorithm-based SR, peak signal to noise ratio (PSNR) (40.08 dB) and structural similarity (SSIM) (0.98) of MRI images were both higher than those of fully connected neural network (FNN) (38.01 dB, 0.93) and recurrent neural network (RNN) (37.21 dB, 0.93) algorithms. Diagnostic sensitivity (95.34%), specificity (75%), and accuracy (94.44%) of MRI images were obviously superior to those of conventional MRI (81.40%, 50%, and 80%). PedsQLTM 4.0 scores of the observation group 1 to 3 months after discharge were all higher than those of the control group ( 54.55 ± 5.76 vs. 52.32 ± 5.12 and 66.32 ± 8.89 vs. 55.02 ± 5.87 ). Sequela incidence in the observation group (13.73%) was apparently lower than that in the control group (43.59%) ( P < 0.05 ). Conclusion. (1) SR-CNN algorithm could increase the definition and diagnostic ability of MRI images. (2) TC could reduce sequelae incidence among SVE children and improve their quality of life (QOL).