This study evaluated the spoilage potential of dominant bacteria (Shewanella putrefaciens and Pseudomonas fluorescens) on the effect of the deterioration of adenosine triphosphate-related compounds in refrigerated large yellow croaker fillets under air-packaging and modified atmosphere packaging (MAP). In this work, the total viable count (TVC), adenosine triphosphate-related compounds, and related enzyme activities were characterized in refrigerated large yellow croaker fillets inoculated spoilage bacteria. Macrogenomic analysis was employed to explore the contribution of packaging methods to metabolic pathways and related enzymes. The result demonstrated that the TVC of S. putrefaciens reached 7.85 (lg (CFU/g)) on day 21, exhibiting stronger potential for growth in MAP. The results showed that S. putrefaciens had a higher potential to degrade adenosine triphosphate-related compounds and produce related enzyme activities under MAP conditions than P. fluorescens. The initial value of hypoxanthine riboside (HxR) during storage in the air processing (AIRP) group was 0.76 μmol/g, which reached a peak on day 3 (1.71 μmol/g), and the level of HxR decreased to 0.38 μmol/g on day 12. The MAP group showed a similar trend to the AIRP group, but the peak appeared later than the AIRP group. The ability to degrade HxR in S. putrefaciens exhibited a significant difference in air packaging. In addition, macrogenomic analysis indicated that the degradation of inosine monophosphate (IMP) was primarily performed by 5'-nucleotidase (5'-NT). This study enhances our comprehension of the role of microorganisms in fish spoilage and provides valuable insights for the development of novel preservation methods.