Cyprinid herpesvirus-2 (CyHV-2), a linear double-stranded DNA virus of the genus Cyprinivirus (family Alloherpesviridae), is a significant pathogenic agent responsible for herpesviral hematopoietic necrosis disease (HVHND), causing severe mortality in cyprinid fishes. While CyHV-2 is well documented in goldfish and crucian carp, information on its pathogenicity in Chinese carps remains limited. The present study investigated a severe disease outbreak in carp polyculture systems, with a focus on Hypophthalmichthys molitrix, integrating epidemiological observations, pathology, molecular characterization, and experimental infection trials. Affected fish exhibited clinical signs, including lethargy, hemorrhages, and respiratory distress, accompanied by extensive gross and histopathological lesions involving the gills, kidney, spleen, and musculature. CyHV-2 was detected by PCR in both diseased and apparently healthy fish, suggesting subclinical infection or transient viral presence. Sequence analysis of the partial DNA polymerase gene showed 94.95% identity with the virulent Asian strain CNDF-TB2015 and clustered within the CyHV-2 clade, confirming the virus identity. Experimental infection using tissue-derived inocula showed differential pathogenicity, with kidney (upto 80%) and gill-derived inocula (70%) inducing significantly higher mortality (log-rank test, p < 0.005) than liver-derived inocula (10%). Bacteriological analysis revealed concomitant Aeromonas infection, suggesting viral-bacterial synergism during disease outbreaks. Collectively, the findings implicate CyHV-2 as a primary viral agent involved in the outbreak and highlight kidney and gill tissues as critical targets for pathogenesis. This study provides the first integrated pathological, molecular, and experimental evidence of CyHV-2 pathogenicity in carp polyculture systems and underscores the need for routine surveillance to mitigate emerging viral threats in aquaculture.