Pyraclostrobin (PYR) is widely used in agriculture to control fungal infestations. However, the toxic effects of PYR on aquatic organisms remain poorly understood. In this study, common carp were exposed to 0.5, and 5.0 μg/L PYR for 30 days to evaluate the chronic effects on gill health via histopathological, biochemical, molecular, and metabolomic analyses. The findings revealed that exposure to PYR resulted in significant histopathological alterations, suppression of mitochondrial complex III activity, and excessive production of reactive oxygen species (ROS), including O2•- and H2O2. Additionally, PYR exposure altered the levels of superoxide dismutase (SOD), catalase (CAT), and glutathione (GSH) while increasing the malondialdehyde (MDA) content in the gills of common carp. The protein expression levels of lysozyme (LZM), tumor necrosis factor alpha (TNF-α), interleukin 1 beta (IL-1β), and transforming growth factor beta (TGF-β) were significantly elevated following exposure to PYR, whereas the levels of complement 3 (C3) and immunoglobulin M (IgM) were decreased. Furthermore, the amount of IL-6 decreased on day 15 before increasing on day 30. Further analysis revealed a notable increase in acid phosphatase (ACP) activity and a decrease in alkaline phosphatase (AKP) activity after 30 days of PYR exposure. Moreover, PYR exposure significantly altered the mRNA expression levels of immune-related genes (lzm, c3, and igm) and apoptosis-related genes (p53, bcl-2, bax, caspase-3, and caspase-9). Several inflammatory markers, such as NF-κB p65 protein and the mRNA levels of tlr2, tlr4, myd88, tnf-α, il-1β, il-6, and tgf-β, were also markedly changed. Metabolomic studies demonstrated that PYR influences pathways related to amino acid, nucleotide, arachidonic acid, and linoleic acid metabolism. These results indicate that PYR adversely affects gill health by inducing oxidative stress, disrupting immune and inflammatory responses, affecting apoptosis-related pathways, and altering metabolic homeostasis. This study provides new insights into the toxic mechanisms of PYR and contributes to the assessment of the ecological risks associated with its presence in aquatic ecosystems.