Autoimmune encephalitis (AE) is a severe neurological disease often accompanied by consciousness disturbances, severe swallowing difficulties, and gastrointestinal dysfunction, increasing the risk of malnutrition. However, the optimal caloric intake target during the acute phase of AE remains unclear. This study aims to evaluate the impact of caloric intake on short-term clinical outcomes in AE patients, specifically focusing on the improvement in Clinical Assessment Scale for Autoimmune Encephalitis (CASE) scores, to provide recommendations for nutritional support during the acute phase. A retrospective study analyzed clinical data from 128 adult AE patients requiring nutritional support, admitted to West China Hospital, Sichuan University, from January 2020 to January 2024. Patients were categorized into low-calorie intake (below 70% of requirements), standard-calorie intake (70-100% of requirements), and high-calorie intake (above 100% of requirements) groups. Multivariate linear and logistic regression models were used to quantify the associations. Higher caloric intake was significantly associated with improved CASE scores (β = 8.58, SE = 3.75, 95% CI = 1.14 to 16.03, p = 0.02). Low caloric intake negatively impacted the improvement of CASE scores (p = 0.049), particularly in seizures and speech problems. The low-calorie intake group had significantly longer hospital stays and nutrition therapy durations (45.79 ± 30.98 days, p < 0.01; 40.39 ± 31.92 days, p = 0.02). Adequate caloric intake has a significant positive impact on the short-term clinical outcomes of AE patients, suggesting that meeting or exceeding caloric requirements may promote neurological recovery in AE patients. Future prospective studies are needed to validate these findings and further optimize nutritional support strategies.