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Tung tree (Vernicia fordii) is one of the important oil plants in China. The current researches on tung tree are mainly focused on the cultivation and breeding while the molecular mechanisms hidden in the back of tung tree's phenotypes are still uncovered. This research compared the transcriptome of three different stages during tung tree's seed development using RNA-Seq and obtained a lot of differentially expressed Unigenes. Through GO classification and pathway enrichment analysis, all of these differentially expressed Unigenes were classified into 128 signaling pathways including fatty acid biosynthesis. Fourteen homologous proteins were obtained when the sequences of 54 Unigenes within fatty acid biosynthesis pathway were aligned against KEGG database and the expression profiles of the genes encoding these proteins during seed development were analyzed. This research provides necessary data platform to elucidate the molecular mechanism underlies fatty acid biosynthesis of tung tree's seeds and theoretical guidance of tung tree varieties' improvement to increase output of tung oil.