As one of the motile species of Aeromonas, Aeromonas veronii is widely distributed in aquatic ecosystems and has been determined as an important pathogen for aquatic in addition to terrestrial animals and humans. In this study, we collected 34 A. veronii isolates from aquatic animals in Sichuan, China. Six housekeeping genes (gyrB, groL, gltA, metG, ppsA and recA) were used for multilocus sequence typing. The results showed that the isolates had high diversity, of which 21 subtypes could be divided into two groups. The group B consisted of 15 new sequence types (ST861-875), and the group A was more closely related to strains from water. Besides, the antibiotic susceptibility of each isolate was determined using the disc diffusion method. Discs of 17 antimicrobial agents were used, including penicillin, cefaclor, cefotaxime, meropenem, amoxicillin, kanamycin, gentamycin, amikacin, neomycin, ciprofloxacin, enrofloxacin, tetracycline, doxycycline, florfenicol, cotrimoxazole, rifampicin, and azithromycin. Most isolates showed resistance to 17 antibiotics such as penicillin, enrofloxacin, and doxycycline. Moreover, high-throughput qPCR was used to detect ARGs of the isolates. A total of 62 ARGs were detected positively based on 95 ARGs detection, in which class aminoglycosides, beta-lactams, and multiple drugs were the most prevalent. Our study indicated that different genotypes showed different distribution of ARPs and ARGs. To our knowledge, this is the first report of molecular subtyping and antibiotic resistance profiles in A. veronii from aquatic animals in Sichuan, these data provide a valuable referee for the prevention and control of corresponding diseases.