The invention relates to a binary fingerprint spectrum of lotus root polysaccharide and a construction method of the binary fingerprint spectrum. The construction method comprises the following steps: crushing three test parts including lotus root skin, edible parts and lotus root nodes respectively; extracting polysaccharide from the crushed three test parts respectively to obtain samples of the lotus root polysaccharide; performing FTIR (Fourier transform infrared spectroscopy) detection and HPLC (high performance liquid chromatography) detection on the samples of the lotus root polysaccharide respectively to obtain infrared spectrums and HPLC maps of the polysaccharide; repeating multiple times to obtain the infrared spectrums and the HPLC maps of the polysaccharide of three test parts including lotus root skin, edible parts and lotus root nodes of different varieties of lotus roots; and constructing by an average vector to obtain an infrared standard fingerprint spectrum and an HPLC standard fingerprint spectrum of lotus root polysaccharide. The invention has an advantage that the infrared standard fingerprint spectrum and the HPLC standard fingerprint spectrum are constructed based on multi-dimensional data of the polysaccharide in lotus root resources; the binary fingerprint spectrum can be used for identification and quality control of polysaccharide from the lotus roots, and has accuracy higher than that of single fingerprint spectrum.