Cell culture liquid waste containing antibiotic resistance genes (ARGs) and microbial community were still not received enough recognition, which pose potential risks to human health. Sixty-eight resistance genes and intl1 were detected in eight samples by Quantitative real-time PCR, while intl1 was only detected in hospital group. Meanwhile, the bacterial community was complex and diverse in each sample by 16S rRNA gene high-throughput sequencing, in addition, Morganella and Enterococcus presented a significant difference between two groups. Whole genome shotgun sequencing revealed that Morganella morganii had more resistance genes and virulence factors in hospital group, and three extended-spectrum beta-lactamase (ESBL) genotypes were found to be blaDHA-5, blaOXA-1, and blaTEM-1. This study provided a preliminary report on ARGs and resistant strains, which reminded people attention to the health risks of potential pathogens in this waste.