A high coverage matrix assisted laser desorption/ionization mass spectrometry imaging(MALDI-MSI) method was developed to visualize the spatial locations of a wide spectrum of metabolites in lotus seed in this paper，in which the spatial locations of alkaloids，flavonoids，amino acids，fatty acids，organic acids,cholines and phospholipids in lotus seed were successfully imaged.Results suggested that the alkaloids are mainly distributed in the lotus seed germ，the flavones are mainly located in the lotus seed germ and lotus seed skin，the levels of amino acids in lotus seed cotyledon are significantly higher than that in the lotus seed embryo，there are few distribution differences of fatty acids in different tissues of lotus seed，the levels of choline in the lotus seed germ and the bottom of the lotus seed cotyledon are higher than those in other tissue regions，glycerophosphocholine mainly distributes in the apex of the lotus seed cotyledon，and the levels of organic acids and most phospholipids in the lotus seed cotyledon are higher than that in the lotus seed embryo.This study provides a new way to investigate the drug quality and the metabolic networks of lotus seed.