The　biological　function　of　HIV-1　integrase　(IN)　is　to　integrate　viral　DNA　into　the　host　cell　chromosome.　and　the　specific　binding　of　IN　with　viral　DNA　is　a　precondition　for　IN　to　function　correctly.　Beforehand,　the　binding　mode　of　IN　dimer　(IN2)　with　the　27　bp　segment　of　viral　DNA　before　3＇　processing　(3＇-P)　was　obtained　via　a　molecular　docking　method.　Based　on　the　binding　mode,　the　aim　of　this　article　was　to　explore　the　changes　of　motive　mode　and　correlative　motion　for　the　IN2　and　DNA　systems　after　their　binding　through　dynamical　cross-correlation　map　(DCCM)　and　principal　component　analysis　(PCA).　Finally,　solvent　effect　during　the　association　was　analyzed　briefly.　The　results　show　that　there　is　a　significantly　increased　positive　correlation　in　the　interface　region　between　IN2　and　viral　DNA,　and　some　obvious　motive　mode　changes　of　the　two　systems　(IN2　and　DNA)　were　also　observed　after　their　binding.　It　was　found　that　water　molecules　played　an　important　role　in　the　recognition　between　IN2　and　viral　DNA　through　analyzing　the　water-mediated　hydrogen　bonds.