Objective To investigate the predictive effect of age-creatinine-ejection fraction (ACEF) score combined with Apelin-13 on coronary artery lesion(CAL) in children with Kawasaki disease. Methods The clinical data of 185 children with Kawasaki disease were retrospectively analyzed, and they were divided into the CAL group (n=35) or the non-CAL group (n=150) according to if complicated with CAL. The clinical data of the two groups were compared, multivariate logistic regression analysis was used to analyze influencing factors of CAL in children with Kawasaki disease, and the receiver operating characteristic (ROC) curve was used to analyze the value of ACEF score combined with Apelin-13 in predicting CAL in children with Kawasaki disease. Results The proportion of children with fever duration >10 days, ACEF score, and levels of C-reactive protein, troponin I, D-dimer, interleukin (IL)-1β, IL-6, IL-10, N-terminal pro-brain natriuretic peptide, and tumor necrosis factor-α in the CAL group were higher than those in the non-CAL group, but the Apelin-13 level, erythrocyte sedimentation rate, and hemoglobin level were lower than those in the non-CAL group (all P<0.05). Multivariate logistic regression analysis results showed that the fever duration, ACEF score, Apelin-13 level, and IL-10 level were influencing factors of CAL in children with Kawasaki disease (all P<0.05). The results of ROC curve analysis showed that the ACEF score and Apelin-13 level had certain predictive values on CAL in children with Kawasaki disease, and the predictive value of their combination was higher than that of one single index. Conclusion The ACEF score and Apelin-13 level are influencing factors for CAL in children with Kawasaki disease, and their combination had a higher predictive value in predicting the occurrence of CAL in children with Kawasaki disease.