Lignans are major bioactive secondary metabolites, which are also formed in the heartwood (hW) of Taiwania (Taiwania cryptomerioides). Their biosynthesis pathways are complex and involve many enzymes and intermediates. To evaluate the extent of the genetic components leading to the variety of lignans in Taiwania hW, 35 Taiwania genotypes of four provenances were surveyed using the proton nuclear magnetic resonance (1H-NMR) and liquid chromatography-mass spectrometry (LC-MS) analyses. The metabolite profiles were statistically evaluated by principal component analysis (PCA) and the general linear model (GLM). The broad-sense heritability (H2) was further evaluated by linear mixed model (LMM) analysis. It was demonstrated that the genetic factor is the major contributor to the abundance of lignans, though the environmental factor also has some effect on it. Among the metabolites detected by 1H-NMR, lignans were the major compounds that exhibited high a H2 (0.52–0.82), which was further verified by LC-MS. The conclusion is that 1H-NMR spectroscopy is suitable for quick screenings, predictions and semi-quantitation of lignans. The high H2 is also indicative of the lignan abundances as traits that can be genetically modified to achieve a significant wood quality improvement.