Purpose To assess the risk factors for surgical site infections (SSIs) post-abdominal surgery in neonates. Methods A retrospective, single-center cohort study was conducted using patient data from 2009 to 2018. Patient characteristics and several variables were analyzed to identify independent risk factors for SSI. Results SSI occurred in 39/406 procedures (9.6%). Univariate analysis showed that the incidence of SSI was significantly higher in patients who had undergone multiple surgical procedures (P = 0.032), prolonged operations (P = 0.016), long-term hospitalization (P < 0.001), long-term antibiotic administration (P < 0.001), with methicillin-resistant Staphylococcus aureus (MRSA) colonization (P = 0.044), contaminated/dirty wounds (P < 0.001), and American Society of Anesthesiologists physical status of 3 or 4 (P = 0.021). Multivariate analysis identified prolonged operations [odds ratio (OR): 2.91 (1.21-8.01)] and contaminated/dirty wounds [OR: 5.42 (2.41-12.1)] as independent risk factors. Patients with SSI had a higher incidence of MRSA colonization (27.8% vs. 14.8%, P = 0.044), longer antibiotic administration (24 days vs. 8 days, P = 0.049), and longer hospitalization times (98 days vs. 43 days, P = 0.007) than those without SSIs. Conclusions Long operations exceeding 100 min and surgical procedures with contaminated/dirty wounds are independent risk factors for neonatal SSIs after abdominal surgery. SSIs were related to MRSA colonization during hospitalization, long-term antibiotic administration, and long-term hospitalization.