It is studied how the α cluster degrees of freedom, such as α clustering configurations close to the α decay threshold in (12)C and (16)O, including the linear chain, triangle, square, kite, and tetrahedron, affect nuclear collective vibrations with a microscopic dynamical approach, which can describe properties of nuclear ground states well across the nuclide chart and reproduce the standard giant dipole resonance (GDR) of (16)O quite nicely. It is found that the GDR spectrum is highly fragmented into several apparent peaks due to the α structure. The different α cluster configurations in (12)C and (16)O have corresponding characteristic spectra of GDR. The number and centroid energies of peaks in the GDR spectra can be reasonably explained by the geometrical and dynamical symmetries of α clustering configurations. Therefore, the GDR can be regarded as a very effective probe to diagnose the different α cluster configurations in light nuclei.