Gingko biloba is currently the only remaining gymnosperm of the Ginkgoaceae Ginkgo genus, and its history can be traced back to the Carboniferous 200 million years ago. Terpene trilactones (TTLs) are one of the main active ingredients in G. biloba, including ginkgolides and bilobalide. They have good curative effect on cardiovascular and cerebrovascular diseases because of their special antagonistic effect of platelet-activating factors. Therefore, it is necessary to deeply mine genes related to TTLs and to analyze their transcriptional regulation mechanism, which will hold vitally important scientific and practical significance for quality improvement and regulation of G. biloba. In this study, we performed RNA-Seq on the root (R), stem (S), immature leaf (IL), mature leaf (ML), microstrobilus (M), ovulate strobilus (OS), immature fruit (IF), and mature fruit (MF) of G. biloba. The TTL regulatory network of G. biloba in different organs was revealed by different transcriptomic analysis strategies. Weighted gene co-expression network analysis (WGCNA) revealed that the five modules were closely correlated with organs. The 12 transcription factors, 5 structural genes, and 24 CYP450 were identified as candidate regulators for TTL accumulation by WGCNA and cytoscape visualization. Finally, 6 AP2/ERFs, 2 CYP450s, and bHLH were inferred to regulate the metabolism of TTLs by correlation analysis. This study is the comprehensive to authenticate transcription factors, structural genes, and CYP450 involved in TTL biosynthesis, thereby providing molecular evidence for revealing the comprehensive regulatory network involved in TTL metabolism in G. biloba.