Studying the pollen morphology of this remnant and endemic wild species of Cathaya argyrophylla can be of use for paleobiologists. During this study, 23 genotypes sampled from four natural populations in two regions of Hunan Province, China. A total of 460 pollen grains were analyzed for seven quantitative and seven qualitative traits (including five new traits). Three quantitative traits (B, P, and A) (Width of the saccus (B); Length of the polar axis (P); Length of the saccus (A)) and four qualitative traits (O-CO, B-SD, O-CSR, and B-SU) (Pollen corpus outlined in the polar distal view (O-CO); Whether the outline of two sacci was distinct or not in the polar proximal view (B-SD); Roughness degree between corpus from the polar proximal view and the sacci from the polar distal view (O-CSR); Whether the overall size of two sacci was uniform or not (B-SU)) were the diagnostic pollen features that could possible to differentiate one population and classified 23 samples into two, three, or four clusters. Furthermore, 24 environmental factors were evaluated and precipitation factors effected more on pollen morphology than geographic and temperature factors, which including annual precipitation (bio12), precipitation of wettest month and driest month (bio13, bio14), precipitation seasonality (bio15) and monthly averaged precipitation in May (05-precip). The main precipitation and temperature factors exhibited positive and negative correlation with pollen size (B and E (Equatorial diameter (E))), respectively. This article provides deeper insight into intraspecific variability of pollen grains of C. argyrophylla, which have been investigated for the first time. In addition, the insights gained from this study could assist with the seed breeding and population reproduction of the endangered C. argyrophylla tree.