Tung tree (Vernicia fordii Hemsl.), widely distributed in China, is a major potential source of biofuel. Exploration of the lipid biosynthesis regulatory network is essential for increasing tung tree lipid yield and its economic value. LncRNAs play significant regulatory roles in many different biological processes in plants. In this study, the profile and differential expression of lncRNAs and mRNAs were evaluated in tung tree seeds in two lipid accumulation phases using high-throughput sequencing technologies. GO function analysis of the protein-coding genes revealed that the majority of up-regulated genes were enriched in the categories of carbohydrate transport (GO:0008643), positive regulation of seed germination (GO:0010030), seed oilbody biogenesis (GO:0010344) and lipid metabolic process (GO:0006629). Network analysis showed that 177 up-regulated lncRNAs might regulate 1290 target genes. GO function analysis was performed on the lncRNA up-regulated target genes, revealed that the lipid particle organization (GO:0034389) was enriched in the biological process. Associated chromatin interactions between lncRNAs and mRNAs were conducted according to Hi-C data. A total of 68 lncRNAs and 46 genes were included in the lipid biosynthesis regulatory network, which provides useful information to reveal the interaction between lncRNAs and coding genes related to lipid biosynthesis in tung tree.