Background/Objectives: Intra-abdominal infections (IAIs) constitute significant clinical challenges that can rapidly progress to life-threatening conditions if not promptly diagnosed and treated. Traditional pathogen identification methodologies, predominantly culture-based, frequently necessitate extended turnaround times (TATs) and exhibit limitations in detecting polymicrobial or anaerobic infections. Methods: We implemented Oxford Nanopore Technology (ONT) sequencing to analyze the microbiota in patients with IAIs at Taichung Veterans General Hospital. The study cohort comprised sixteen patients with IAIs. Following specimen collection, DNA extraction was performed, and then full-length 16S rRNA and ITS region amplification and subsequent ONT sequencing were conducted. Results: Conventional clinical culture-based methodologies detected pathogens in 13 patients. Among the 14 successfully sequenced specimens, ONT sequencing elucidated a diverse spectrum of bacteria and fungi, with read counts ranging from 375 to 19,716. Polymicrobial and anaerobe-enriched communities were predominantly observed in lower gastrointestinal tract infections, specifically colonic or small bowel perforations, whereas upper gastrointestinal perforations, including those of the stomach or duodenum, were frequently dominated by Streptococcus, Granulicatella, or Candida species. The sequencing identified pathogens concordant with culture results, including Escherichia coli, Enterococcus, and Candida albicans. In addition, anaerobic or low-abundance taxa were exclusively identifiable through sequencing methodologies. Conclusions: ONT sequencing facilitated results within up to 24 h and successfully detected pathogens in culture-negative cases. These findings underscore the utility of ONT sequencing as an expeditious and comprehensive diagnostic modality for IAIs.