Many leaf fossils belonging to Quercus sect. Heterobalanus were collected from the Upper Pliocene Sanying Formation in Heqing County, Yunnan Province, China. Leaves are oblong, elliptic or obovate with entire margin or spinous serrations, 3.1–8.7 cm in length and 1.8–5.7 cm in width. Leaf apex is round, mucronate or blunt round, while leaf base is heart-shaped, slightly heart-shaped or blunt round, and occasionally asymmetric. The petiole is slightly sturdy, straight or a bit curved, with 1.8–4.9 mm in length. The main vein of these specimens is slightly zigzagging, with a sturdy base attenuating to the apex. Secondary veins are pinnate, 7–12 pairs, alternate and parallel with the stretching angles from 40° to 73°, bifurcating near 1/3 to 1/2 of the leaf margin. Tertiary veins are, relatively thin, 5–7 bands in 1 cm2, and perpendicular to secondary veins. Quaternary, blind and marginal veins are not clear. The upper epidermis has both unicellular and multicellular trichomes without stomata, and most of the epidermal cells are nearly quadrangular. The lower epidermis has only unicellular trichomes and cyclocytic stomatal apparatuses, and the epidermal cells are nearly quadrangular or pentagonal. The stomatal apparatuses are 20–33 m m in length, 17–27 m m in width , with 2–6 m m wide in apertures. They spread casually with the stomatal density of 503±98 mm - 2 and the stomatal index of 8.90%±0.32%. The guard cells show kidney-shaped, with 5–7 subsidiary cells. These features are similar to Q. rehderiana, Q. guyavifolia , Q. preguyavifolia and some other extant or fossil species of Q . sect. Heterobalanus , but they are different in terms of density and type of trichomes. Both Q . guyavifolia and Q . preguyavifolia have more trichomes in total, and multicellular trichomes in lower epidermis which spread in veins and between veins. The fossil leaves of Q . sect. Heterobalanus in Heqing and Q . rehderiana have less trichomes, and the former has no multicellular trichome in lower epidermis, while the latter’s multicellular trichome are just found in veins. Hence, it was designated as a new species— Quercus heqingensis n. sp. The estimates of palaeoatmospheric-CO2 using the positive relationships between stomatal frequency and atmospheric CO2 partial pressure in its Nearest Living Relatives (NLRs)— Q . guyavifolia show that, the palaeo-CO2 levels in the late Pliocene reconstructed by Q. heqingensis were 263.42±24.86 ppm (equation with extant field collections) and 234.25±22.49 ppm (equation with historical herbarium samples). These results are slightly lower than most previous estimates of the same age. Our results are in agreement with other estimates when palaeoaltitude is considered. This indicates that it is feasible to apply the stomatal index of Q . heqingensis to the positive relationship between stomatal index of Q . guyavifolia and atmospheric p CO2 to reconstruct palaeo-CO2 levels. Meanwhile, the results further support lower palaeo-CO2 level in the late Pliocene than present. This study provides credible evidence for future palaeo-CO2 estimates using NLRs as proxies.