Sexual dimorphism is well-documented in aquaculture, particularly regarding growth differences, wherein one sex often grows faster than the other. However, despite the phenomenon being so widely documented, its underlying molecular mechanisms remain poorly understood. As an important digestive and immune organ, the gut plays key roles in the regulation of fish growth. In this study, we conducted RNA-seq and metabolomic analysis on the gut of female and male common carp. We discovered that growth-related pathways, such as "Glycolysis/Gluconeogenesis" and "Riboflavin metabolism" are significantly enriched in the gut of female carp. Conversely, pathways linked to disease resistance, such as "Th17 cell differentiation" and "Autophagy-animal" are predominantly enriched in male carp. Following intraperitoneal injection of spring viraemia of carp virus (SVCV) into both male and female carp, quantitative reverse transcription polymerase chain reaction (RT-qPCR) analysis and histopathological staining confirmed that male carp exhibit greater disease resistance compared to females. This study identified the disease resistance dimorphism in common carp and specific mechanisms underlying growth differences. Our findings offer valuable insights for the application of growth dimorphism and disease-resistant breeding in fish.