Fritillaria Bulbus (FB) is a medicinal food homologous substance containing various alkaloids. However, the authenticity and quality control of FB have been regarded as the important and challenging factors in globalization and modernization. In this study, the spatial distributions of alkaloids from four FBs ( Fritillaria thunbergii Miq, FritiLlaria cirrhosa D. Don, Fritillaria ussuriensis Maxim, Fritillaria unibracteata var. wabuensis) were analyzed by a consolidation of UPLC-Q-Extractive Orbitrap MS/MS and direct desorption electrospray mass spectrometry imaging (DESI-MSI). Results showed that 58 reliable metabolites (mainly alkaloids) were identified preliminarily, and taxonomic models were built by chemometric analysis. The alkaloid contents in the bulb base were significantly higher than those in bulb and bulblet ( p < 0.05). Seven metabolites, hexadecanamide, imperialine, L-phenylalanine, jervine, peimine, L-pyroglutamic acid, and trans-3-indolacrylic acid, were screened and confirmed as key characteristic compounds of FB. The detailed spatial information provides a reliable means for rational evaluation of the quality control of FBs. It can better utilize the enriched portion of the alkaloids in FBs. It can provide reference value for the identification of adulteration and development of the medicinal food homologous substance. • A total of 58 compounds were characterized from FB at four different species. • UPLC-Q-Exactive Orbitrap MS/MS and DESI-MSI methods were combined for analyzing FB. • Imperialine, jervine, and peimine are the characteristic pharmacological alkaloids of FB. • Bulb base is a hotspot for alkaloid enrichment in FB. • Different alkaloids of FB could be visualized by DESI-MSI in situ.