The polarization dependence of excitation light for fluorescence enhancement of near-infrared dyes immobilized in hydrophobic DNA thin film on glass substrates with regularly arranged Au nanoblocks was investigated. The enhancement factor for S-polarized excitation was about 1.2 to 1.5 times as large as that for P-polarized excitation. P-polarized light contributed to the excitation of plasmon band both of horizontal and vertical direction of Au nanoblocks. The vertical direction corresponds to the short axis for height direction which has the absorption in visible region did not contribute the excitation of IR780. When the absorption band of Au array and the fluorescence band of IR780 were overlapped, the fluorescence enhancement did not depend on the polarization of excitation light. It is suggested that the fluorescence quenching originates from the energy transfer from the excited state of IR780 to Au nanoblocks or the increased deactivation of excited dye molecules induced by resonance with Au nanoblocks.