Background: Cyclocarya paliurus (Batal.) Iljinskaja is a common endemic tree species. The leaves of C. paliurus are used as a Chinese medicine and the main active components are polysaccharides. However, the temporal pattern of polysaccharide synthesis at different leaf developmental stages has not been reported to date. Results: With the development of leaves, the content of polysaccharides increased first and the highest content was found at the F3 stage (the third larger full expanded leaf). A total of 499710194 clean reads were obtained using C. paliurus genomic data and were assembled into 296593 unigenes. Among 4708 identified DEGs, 429 DEGs were up-regulated and 451 DEGs were down-regulated from F1 stage (the smallest full expanded leaf) to F2 stage (the second larger full expanded leaf), 630 DEGs were up-regulated and 60 DEGs were down-regulated from F2 stage to F3 stage, and 1833 up-regulated and 1816 down-regulated DEGs from F3 stage to F4 stage. Forty DEGs associated with GT belong to 13 GT families. Among them, only one gene was down-regulated from F1 stage to F2 stage, two genes were down-regulated from F2 to F3 stages, and 23 genes were down-regulated and 15 genes were up-regulated from F3 stage to F4 stage, respectively. A significant correlation exists between the five unigenes and the polysaccharide content. UDP-glucose 4-epimerase gene was significantly positively correlated with the polysaccharide content. A pathway map for the biosynthesis of C. paliurus polysaccharide was proposed. Among 150 transcription factors identified from DEGs, the majority was members of the AP2/ERF family (21, 14%), followed by the C2H2 family (14, 9.33%), the MYB family (12, 8%), the C2C2-GATA family (10, 6.67%), the GRAS family (9, 6%), and the zf-HD family (7, 4.67%). Conclusions: These results identified genes involved in the biosynthesis of Cyclocarya paliurus polysaccharides during different leaf developmental stages and provided evidence for the change of polysaccharide content during the development of C. paliurus leaves. Possible synthetic pathways and related transcription factors were suggested. This study provides information for the screening of polysaccharide biosynthesis related genes and elucidates the mechanism underlying polysaccharide biosynthesis in C. paliurus.