In order to improve the stability of Traditional Chinese Medicine′s fluorescence fingerprint spectra of constructing images and data processing efficiency, Liquid Crystal Spectrometer was used to detect spectral image of Cortex Phellodendri and Total Saponins of Panax Ginseng. Effective pixels were extracted using the combination of filter and localizing pixels means, besides, their pixels′ spectral images were obtained to draw Traditional Chinese Medicine′s fluorescent fingerprints correspondingly. Considering their Euclidean distance, when compared the three methods, the combination of filter and localizing pixels means has the best fluorescence fingerprint and spectral stability, followed by the background differencing, then is the optimization of pixels. By experimental results, it is revealed that spectral stability by this way is better and can be used to build Traditional Chinese Medicine′s fluorescent fingerprints. Based on these points, a new approach used for collecting effective pixels during Traditional Chinese Medicine′s fingerprints construction is proposed.