Objective To identify and quantify independent risk factors for poor perioperative outcomes in neonates with transposition of the great arteries (TGA) and arterial switch operation (ASO), and establish a predictive model for risk stratification and perioperative management optimization. Methods A retrospective analysis was conducted on the clinical data of neonatal TGA patients treated with ASO at Guangdong Provincial People's Hospital from January 1998 to August 2024. The research variables included baseline characteristics, preoperative parameters, surgical variables, and postoperative management indicators. The main outcome was perioperative composite adverse events. Multiple logistic regression was used to screen for independent risk factors and construct a predictive model. Results Finally, 376 patients were enrolled, including 306 (81.4%) males and 70 (18.6%) females, with a median gestational age of 39 weeks and an average age of visit of (3.86±5.76) days. The 167 (44.4%) patients experienced poor prognosis. Low admission length [OR=0.726, 95%CI (0.643, 0.815)], low preoperative oxygen saturation [OR=0.942, 95%CI (0.922, 0.962)], and longer cardiopulmonary bypass time [OR=1.85, 95%CI (1.189, 2.887)] were independent predictive factors of postoperative ASO. The predictive model had good discriminative ability (area under the curve=0.800). Conclusion The short-term poor prognosis of TGA neonatal ASO surgery is highly correlated with admission length, preoperative hypoxia, and longer extracorporeal circulation time. Early risk stratification based on these readily available clinical parameters can aid in individualized perioperative management and improve prognosis.