Neurological complications (NC) are frequent complications after liver transplantation (LT). We aim to assess the association between single nucleotide polymorphisms (SNPs) and new-onset neurological complications after liver transplantation. This study contributes to the prediction of NC and the quality of life of patients after LT. A total of 197 patients who accepted LT surgery at the Affiliated Hospital of Qingdao University were selected. The clinical symptoms and laboratory tests were used to analyze whether the recipients had neurological complications. Genomic DNAs were extracted from donor’s fresh frozen liver and recipient’s anti-coagulated blood using different kits. Categorical variables were compared by Pearson’s χ2 test or Fisher’s exact test, and validated by subsequent logistic regression analysis. Preoperative hepatic encephalopathy as a risk factor for NC was evaluated by logistic regression analysis. In our study, we found five single nucleotide polymorphisms are closely associated with neurological complications, including recipient STK38L/rs2242185 [OR=0.192(0.061-0.605); p=0.005], recipient TNF-α/rs1800629 [OR=2.869(1.006-8.178); p=0.049], recipient MTRR/rs1802059 [OR=6.72(1.229-36.738); p=0.028], donor OATP/rs2306283 [OR=3.425(1.161-10.108); p=0.026], and recipient TNFRSF11A/rs2277731 [OR=0.29(0.107-0.783); p=0.015]. The incidence of NC was 11.17% (22/197), but there was no correlation between preoperative hepatic encephalopathy and postoperative neurological symptoms [OR=1.467(0.393-5.474); p=0.568]. The five polymorphisms are associated with an increased risk of NC after LT and have a potential clinical value for the prediction and prevention of NC.