Marine aquaculture frequently encounter challenges associated with co-infections involving a spectrum of pathogens, which causing disease outbreaks. The multifaceted interactions between these pathogens and their hosts are not well characterized. In this study, we investigate the effects of co-infection by RGNNV and V. rotiferianus on golden pompano. Our findings indicate that co-infection significantly diminished the survival rate and intensified histopathological lesions in the brain, eye, liver, and spleen. Additionally, it facilitated the replication of both pathogens in a broader range of tissues, including the brain, eye, liver, spleen, skin, and muscle. To delve into the immune response mechanisms, we employed neutrophil markers and conducted a transcriptomic analysis. Neutrophil labelling revealed that co-infection mitigated the immune cell proliferation and aggregation in the liver and spleen, which are typically induced by RGNNV alone. The transcriptomic data corroborated these findings, highlighting the significant down-regulation of key immune factors such as IL-8, IL11, IL-1, CNTF, and C1R in brain tissues, and IL-8, IL-1, G-CSF, DCR3, and GADD45 in immune tissues (a mixture of liver and spleen tissues). These genes are pivotal in orchestrating the early inflammatory response and immune processes, including neutrophil proliferation, migration, aggregation, and degranulation. Our results suggest that co-infection may suppress the initial inflammatory response and dampen the activity of principal immune cells, consequently impairing the host's immune defenses and promoting pathogen replication and pathogenicity. In conclusion, the study demonstrates a synergistic interaction between RGNNV and V. rotiferianus in exacerbating the pathogenicity in golden pompano. This research provides foundational insights into the disease risks associated with co-infections, contributing to a better understanding of the underlying immunopathological mechanisms and potentially informing future disease management strategies in aquaculture.