Objective To provide reference for clinical diagnosis and treatment of persistent bloodstream infection caused by carbapenem-resistant Klebsiella pneumoniae (CRKP). Methods This paper reports the anti-infection treatment process of a patient with persistent bloodstream infection caused by CRKP. Clinical pharmacists participated in the development of selective digestive decontamination (SDD) scheme to assist anti-infection, therapeutic efficacy was monitored and long-term follow-up after discharge was conducted. Results after SDD adjuvant treatment, patient’s blood culture turned negative, condition was improved, and he was discharged from hospital. Six-month follow-up showed that the patient recovered well. Conclusion SDD adjuvant treatment may have therapeutic value for persistent bloodstream infection originating from the digestive tract, which is helpful to control the infection of such patient.