The increasing demand for precious timber resources promotes immediate efforts to develop high-valuable hardwood resources in afforestation. However, the lack of valuable tree species seedlings for afforestation and their ecological adaptability must primarily be addressed. To explore a valuable tree species for precious timber resourcing in afforestation, a comparative analysis of the characteristics of photosynthetic physiology and leaf anatomy in three different Quercus L. Section Cyclobalanopsis seedlings of Quercus chungii, Quercus gilva, and Quercus glauca was performed during three growth stages (July, September, and November) in South China. The results showed that there are significant differences in photosynthetic physiological characteristic parameters, chlorophyll content, and leaf anatomical structure among the three seedlings in each growth stage (p < 0.05). The photosynthetic parameters, i.e., Pn, Gs, Tr, WUE and Ci in each tree species all had the same trend of increase from July to September and decrease from September to November, and with a pick point in September during the three stages. The Pn in Q. chungii was higher than that in the other two species in each stage, and the highest Pn with an average value of 8.26 μmol·m−2·s−1 was obtained in September in Q. chungii, which was 13.77% and 20.06% higher than that of in Q. gilva and Q. glauca at the same time, respectively. Significant differences were also detected in the chlorophyll fluorescence of Fo, Fm, Fv/Fm, Y, ETR, qP, and NPQ among three seedlings within each growth stage from July to November (p < 0.05). The thickness of the mature leaf was decreased in order as Q. chungii, Q. glauca, and Q. gilva. From July to September, more notable changes were observed in Q. chungii in September, with a drop of 3.49% in leaf thickness, and a drop of 3.34% and 10.06% in the volume of palisade tissue and sponge tissue, respectively. Consequently, increasing tightness and deducing looseness were observed in Q. chungii. The principal component analysis (PCA) on photosynthesis and leaf anatomy showed that Q. chungii displayed a stronger photosynthetic physiology with a positive coordination on water, air, light, and heat. These findings facilitate the evaluation of ecological adaptability among the three Quercus seedlings and provide compelling evidence for the application of Q. chungii for precious timber resources in afforestation.