Objective To investigate the distribution of pathogens and change of homology of Acinetobacter baumannii (AB) in intensive care units (ICUs) of partial medical institutions in Shanghai before and after the pandemic of coronavirus disease 2019 (COVID-19). Methods Pathogens were isolated and identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), the whole genome of AB was sequenced using Illumina Miseq sequencing platform, and its genetic relationship was explored based on multilocus sequence typing (MLST) and core genome multilocus sequence typing (cgMLST). Results The total detection rate of pathogens in ICU environment after the pandemic was lower than before the pandemic ([6.10%, 101/1 656] vs [10.77%, 181/1 680]; P＜0.05). Before and after the pandemic, the proportion of AB detected on the surface of bedding in the ICU environment remained at the highest level. After the pandemic, the ST types showed a diverse distribution. MLST_Pasteur Results showed that 162 strains of AB were divided into 20 ST types, with ST2 (80.25%, n=130) being the main type. MLST_Oxford Results showed that there were 19 ST types among 162 strains, with ST208 (37.04%, n=60) being the main type. The clustering analysis based on cgMLST showed that ST208_Oxford had closer genetic relationship with ST540_Oxford and ST369_Oxford after the pandemic. ST164_Pasteur clone changed from ST234_Oxford before the pandemic to ST1418_Oxford after the pandemic, and 2 new types of ST_Pasteurr and 11 new types of ST_Oxford were discovered. Conclusion The detection rate of pathogens from ICU environment after the pandemic is lower than before the pandemic, and the distribution of ST types is slightly different at the same detection sites before and after the pandemic. ST2_Pasteur/ST208_Oxford is still the dominant epidemic clone before and after the pandemic, but some alleles have changed. cgMLST is more accurate than MLST_Oxford and MLST_Pasteur in homology analysis, evolution, spread, and outbreak analysis.