Quantonenpollenites, a pollen taxon which was assumed to be angiosperm, is of great significance in confirming the geological age of its bearing strata. Aims to clarify the taxonomic affiliation of Quantonenpollenites, we investigated the external morphology and internal structure using Light Microscopy (LM), Scanning Electron Microscopy (SEM), and Transmission Electron Microscopy (TEM). According to TEM observations, the exine of Quantonenpollenites pollen is unstratified with the absence of a columellar layer, and the exine is tightly connected with the intine. Based on comprehensive morphological evidence, especially the lack of columellar layer which is typical characteristics existing in almost all angiosperm pollen, the botanical affinity of Quantonenpollenites should be attributed to gymnosperms rather than angiosperms as previously thought. Through comparative analysis, it may have a close affinity with Ephedra, but further analytical data are still needed for verification. As a characteristic palynological type of the Quantou Formation in the Songliao Basin, the occurrence of Quantonenpollenites has indicative significance for determining the age of the hosting strata. By systematically clarifying the phylogenetic affiliation of Quantonenpollenites, together with the other associated palynomorphs, this study provides crucial reference materials for defining the stratigraphic age range of the Quantou Formation (Cenomanian to early Turonian), improves the resolution of stratigraphic age calibration of the Quantou Formation, and provides key paleontological evidence for the refined division of the terrestrial Cretaceous chronostratigraphic framework in the Songliao Basin.