The complex (IN_L708, 906) model of HIV-1 integrase with L708, 906 inhibitor was obtained via molecular docking method in previous work. The key residues of IN_L708, 906 complex model were detailedly analyzed from the three perspectives (i.e. distance, energy and hydrogen bond). The results show that the complex model is similar to the IN_5CITEP complex structure from proteins data bank. The difference of the motion modes and correlativity between IN_L708, 906 model and IN monomer was investigated with principal component analysis and dynamical cross-correlation map methods. The computational results indicate that the association with L708, 906 leads to the flexibility decrease of functional loop region, the lose of regular motion, as well as the disordered increase of correlative motion, which may be the main reasons for the activity attenuation of IN. All the simulation results may help the anti-HIV drug design based on the structures of Aryl diketoacids.