Abstract: The IR fingerprint spectra of three different woods, Populus tomentosa，Platycladus orientalis and Ginkgo biloba L., were analyzed by IR Spectroscopy.The structure characters of IR fingerprint spectra of six Ginkgo clones were also analyzed and differentiated by Dual-Index Sequence Analysis of common peak ratio and variant peak ratio. The results shows that The spectral features of these three woods are distinctively different. And the IR fingerprint spectra of Ginkgo wood have the two characters of broadleaf tree and conifer tree,comparatively speaking, more close to the conifer tree.The IR fingerprint spectra of six Ginkgo clones wood are distinctively different, and can be identified through Dual-Index Sequence Analysis of common peak ratio and variant peak ratio.