Upon virus infection into a cell, the uncoated DNA is usually blocked by the host intrinsic immune system inside the nucleus. Although it is a crucial necessary mechanism for virus to counter act with host intrinsic immune system and access its genome, little is known about how viruses can knock down host restriction and identify their blocked genomes for later viral gene activation and replication. We found that upon virus infection, the invading viral DNA is trapped by the cellular death domain-associated protein (Daxx) and histone H3.3 in the nucleus resulting gene inactivation. IE2, a baculovirus transactivator, targets host Daxx through IE2 SUMO-interacting motifs (SIMs) to indirectly access viral DNA, and forms unique nuclear body structures, we name it as clathrate cage-like apparatus (CCLA), at the earlier transduction stages. At the later transduction stage, CCLA gradually enlarges, and IE2 keeps on closely interacting with viral DNA but no longer associate with Daxx at the later transduction stages. The association with Daxx is essential for IE2 CCLA formation, then, the enlarged CCLAs are capable to transactivate viral but not host chromosomal DNA. Our study reveals that baculovirus IE2 counteracts with host intrinsic immune system by specifically targeting Daxx and H3.3 to associate with viral DNA indirectly and efficiently. IE2 then utilizes this association with viral DNA to establish a unique CCLA cellular nanomachinery, which is visible under light microscopy, as an enclosed environment for proper viral gene expressions.