Jujube (Ziziphus jujuba Mill.) honey, one of the most valuable honey varieties from China with unique characteristics, is vulnerable to being the target of adulteration and deliberate mislabeling of botanical origin. This study investigated the typical protein component of jujube honey to authenticate the floral source by SDS-PAGE analysis combined with LC-MS/MS identification, and its stability to heating was also evaluated. One band and two adjacent but independent bands, both with molecular weights of ~19 kDa, were notably observed in Coomassie brilliant blue- and silver-stained SDS-PAGE gels, respectively, for jujube honey from different geographic origins, whereas that was not present for other five botanical honey varieties, suggesting this protein component was suitable as marker for jujube honey. LC-MS/MS identification revealed that it was constituted by one Z. jujuba-derived protein (gene number:Zj.jz016003045) and two A. mellifera-derived proteins (an uncharacterized protein with accession number tr|A0A088AC16 and a cleavage fragment from major royal jelly protein-1), and the existence of plant-derived protein was attributed to the special neutral pH of jujube honey. Additionally, these protein markers exhibited good stability to heating below 85°C/30 min. This study provided a simple method to characterize jujube honey, and firstly identified protein indicator to determine the botanical origin of honey.