In a previous work, gold nanoclusters (Au NCs) are found to inactivate RNA virus, but the effect of surface modification of Au NCs on its proliferation is still largely unknown. Here, the effect of surface modification of Au NCs on the proliferation of pseudorabies virus (PRV) by synthesizing two types of gold clusters with different surface modification, histidine stabilized Au NCs (His‐Au NCs) and mercaptoethane sulfonate and histidine stabilized Au NCs (MES‐Au NCs), is investigated. His‐Au NCs rather than MES‐Au NCs could strongly inhibit the proliferation of PRV, as indicated by the results of plaque assay, confocal microscopic analysis, Western blot assay, and quantitative real‐time polymerase chain reaction (PCR) assay. Further study reveals that His‐Au NCs perform the function via blockage of the viral replication process rather than the processes of attachment, penetration, or release. Additionally, His‐Au NCs are found to be mainly localized to nucleus, while MES‐Au NCs are strictly distributed in cytoplasm, which may explain why His‐Au NCs can suppress the proliferation of PRV, but not MES‐Au NCs. These results demonstrate that surface modification plays a key role in the antiviral effects of Au NCs and a potential antiviral agent can be developed by changing the Au NC surface modification.