The　complex　model　structure　of　human　immunodeficiency　virus-1　(HIV-1)　DNA　with　integrase　(IN)　dimer　ONO　was　refined　through　Molecular　dynamics　(MD)　simulation,　and　the　viral　DNA　conformational　change　was　explored　after　binding　with　IN2.　The　result　showed　that　the　viral　DNA　could　be　divided　into　five　regions　(i.e.　non-binding　region.　high-affinity　region　1,　weak-affinity　region,　high-affinity　region　2,　and　reaction　region)　according　to　the　binding　power　with　IN2.　The　partition　rationality　for　viral　DNA　was　confirmed　through　binding　free　energy　Computation.　Compared　with　the　viral　DNA　before　binding　with　IN2,　some　big　conformational　changes　occurred　for　the　bases　in　the　four　binding　regions　other　than　the　non-binding　region　for　the　viral　DNA　complexed　with　IN2.　The　obvious　deviation　from　standard　B-DNA　in　the　viral　DNA　main　chain　of　the　complex　and　the　broading　of　the　minor　groove　in　the　binding　site　were　both　the　structural　basis　for　the　recognition　of　viral　DNA　with　IN.　The　Simulation　results　basically　agreed　with　experimental　data,　which　provided　some　structural　information　for　the　drug　design　based　on　the　structure　of　HIV-1　IN.