Bloodstream infections (BSIs) caused by multidrug resistant Pseudomonas aeruginosa (MDRPA) and carbapenem resistant Pseudomonas aeruginosa (CRPA) accounted for high morbidity and mortality. This retrospective cohort study aimed to determine risk factors for MDRPA and CRPA BSIs by examining both clinical and laboratory data of inpatients with MDRPA and CRPA BSIs at two tertiary care hospitals in 2017-2021. Generalized linear mixed models were used to identify risk factors for MDRPA and CRPA BSIs. Factors significantly associated with both MDRPA BSIs and CRPA BSIs included central venous catheter, invasive ventilation including duration of use, urinary catheterization, gastric tube insertion, vancomycin use including quantity of usage, imipenem use including quantity of usage, and tigecycline use. Respiratory infection [adjusted odds ratio (aOR) 2.10, 95% confidence interval (95% CI) 1.00-4.42; P = 0.049] was identified as an independent risk factor for MDRPA BSIs. For CRPA BSIs, independent risk factors included the use of invasive ventilation [aOR 2.82, 95% CI 1.36-5.84; P = 0.005] and a history of tigecycline use [aOR 3.34, 95% CI 1.16-9.58; P = 0.025]. Conversely, circulatory system diseases [aOR 0.41, 95% CI 0.22-0.77; P = 0.006] and quantity of piperacillin-tazobactam use [aOR 0.83, 95% CI 0.72-0.96; P = 0.013] were identified as independent protective factors for CRPA BSIs. Inpatients with respiratory infection, invasive ventilation and a history of tigecycline use are at higher risk of MDRPA and CRPA BSIs. More prudent clinical interventions and antimicrobial therapy should be implemented to inpatients with these factors to prevent and control MDRPA and CRPA BSIs.