Objective To establish a novel stratified framework for classifying the co-occurrence of carbapenem-resistant Acinetobacter baumannii (CRAB) and carbapenem-resistant Klebsiella pneumoniae (CRKP), and to characterize its frequency, distribution, and associated factors. Methods A retrospective study was conducted among patients with microbiological results positive for CRAB and/or CRKP at West China Hospital, Sichuan University, and West China Tianfu Hospital, Sichuan University in 2025. Based on the interval between specimen collection dates, CRAB-CRKP co-occurrence was classified as confirmed co-occurrence (same day), probable co-occurrence (≤2 days), or possible co-occurrence (>2 days). Co-occurrence sites were also categorized. Descriptive analyses were performed to characterize CRAB and CRKP detection, and multivariable logistic regression was used to identify factors associated with CRAB-CRKP co-occurrence. Results A total of 2421 patients were included, of whom 347 (14.3%) had CRAB-CRKP co-occurrence, including 237 (9.8%) with confirmed co-occurrence, 14 (0.6%) with probable co-occurrence, and 96 (4.0%) with possible co-occurrence. Among the 347 patients with co-occurrence, 274 (79.0%) had CRAB and CRKP detected at the same anatomical site. A total of 694 relevant specimens were included, of which 571 (82.3%) were respiratory specimens. Multivariable logistic regression showed that trauma was independently associated with CRAB-CRKP co-occurrence [odds ratio (OR)=2.01, 95% confidence interval (CI) (1.09, 3.70), P=0.025]; compared with the combined group of other departments, admission to the Neurology Center [OR=3.28, 95%CI (1.88, 5.73)], Department of Respiratory and Critical Care Medicine [OR=2.76, 95%CI (1.77, 4.31)], Trauma Center [OR=2.47, 95%CI (1.37, 4.45)], Department of Intensive Care Medicine [OR=2.32, 95%CI (1.56, 3.43)], and Emergency Department [OR=1.96, 95%CI (1.35, 2.86)] was significantly associated with CRAB-CRKP co-occurrence (P<0.05). Conclusions CRAB-CRKP co-occurrence was relatively common among patients with CRAB and/or CRKP detected in the two hospitals, with confirmed co-occurrence and detection at the same anatomical site being the predominant patterns. Respiratory specimens were the major specimen type. Trauma and admission to the Neurology Center, Department of Respiratory and Critical Care Medicine, Trauma Center, Department of Intensive Care Medicine, and Emergency Department were independently associated with CRAB-CRKP co-occurrence.