IL-10, an anti-inflammatory cytokine, plays crucial roles in the context of infectious inflammatory diseases, whose gene variations and expression are tightly linked to disease resistance in animals. However, there is limited research on the genetic variations governing IL-10 expression and the underlying effects in fish. In this study, we identified a GAGTT insertion/deletion (Ins/Del) variation within the IL-10 gene promoter and analyzed the effects of this variation on IL-10 expression, inflammatory response and its association with disease resistance in grass carp. With dual luciferase reporter assays, we demonstrated that the GAGTT Ins/Del variation significantly altered the IL-10 promoter activity in grass carp. DNA pull-down combined with mass spectrometry revealed that the spectrum of transcription factors that bind to IL-10 promoter variants caused by GAGTT Ins/Del variation was quite different. Moreover, three representative transcription factors, JunD/AP-1, p50/NF-κB, and HMGB1, differentially transactivated grass carp IL-10 promoter variants, as confirmed by western blotting and dual luciferase reporter assays. Using the GAGTT/− genotype of the heterozygous grass carp parents, we obtained full-sib family offspring of the GAGTT/GAGTT, GAGTT/−, and −/− genotypes. During grass carp reovirus (GCRV) infection, these three IL-10 genotypes of grass carp offspring displayed different survival rates. Importantly, grass carp with the GAGTT/− genotype had greater survival than those with the other two genotypes after GCRV infection. Furthermore, the results indicated that the improved intestinal inflammation at 1 d post-GCRV infection and enhanced immunocompetence in the spleen at 5 d post-GCRV infection may contribute to the disease resistance of grass carp with the GAGTT/− genotype. Overall, this study offers new insight into the inflammatory and immune regulatory mechanisms specific to IL-10 from a genetic perspective in fish and may provide a valuable molecular marker for breeding disease-resistant grass carp.