The human intestinal tract is considered the most important reservoir of the opportunistic pathogens, includingPseudomonas aeruginosa,which is often overlooked but critical due to its antimicrobial resistance and virulence. Public health interventions to control this pathogen require a comprehensive understanding of its epidemiology and genomics.  In the current study, we identifiedP. aeruginosastrains from 2,605 fecal samples collected between 2021 to 2022. Among these samples, 574 were from ICU inpatients in Zhejiang province, while 2,031 were obtained from healthy individuals residing in ten different provinces in China. The prevalence ofP. aeruginosaintestinal carriage was found to be higher in ICU inpatients (10.28%, 95% CI: 7.79%–12.76%) than that in healthy individuals (3.99%, 81/2,031, 95% CI: 3.14%–4.84%). Similarly, the prevalence of carbapenem-resistantP. aeruginosa(CRPA) was higher in ICU inpatients (32.2%) compared to healthy individuals (7.41%). The population structure analysis of our isolates revealed a predominantly non-clonal distribution, with 41 distinct sequence types identified among 59P. aeruginosaisolates from ICU inpatients and 38 different STs among 81P. aeruginosaisolates from healthy individuals. These findings suggest that the individual acquisition ofP. aeruginosais more frequent than patient-to-patient transmission, as evidenced by the polyclonal population structure. Antimicrobial susceptibility testing and genome analysis indicated thatP. aeruginosastrains from ICU inpatients exhibited significantly higher resistance rates to most antimicrobials and harbored a greater number of acquired resistance genes compared to strains from healthy individuals. Notably, in ICU inpatients, we identified three isolates of ST463, all of which shared the conserved Tn3-TnpR-ISKpn8-blaKPC-ISKpn6genetic context. Additionally, five isolates carrying theqacE gene were also identified, these findings suggest that small-scale transmission events may still occur within the ICU setting, posing significant challenges for clinical management. With regard to virulence factors, we observed similar profiles between the two groups, except forphzA2,phzB2,andpilA, which were statistically higher in isolates from healthy individuals. This may be because the accumulating resistance mutations in ICU-derivedP. aeruginosaare linked to a decrease in virulence.