A rare medicinal fungus called Taiwanofungus camphoratus gives people resistance to illness. In order to effectively obtain high−quality T. camphoratus mycelia, we added Cymbopogon citratus (lemongrass) water extract (LWE), which was prepared using hot water and dry lemongrass leaves and methyl jasmonate (MJ) as an additive, in order to cultivate T. camphoratus mycelia. The components of LWE were identified by gas chromatography–mass spectrometry as glucose (61.66%) and galactose (17.10%). Compare to the basal medium, 0.5–2.5 g·L−1 LWE and 5–25 μmol·L−1 MJ can enhance the proliferation of mycelia and the metabolism of polyunsaturated fatty acids (PUFAs). Among them, the T. camphoratus mycelia growth rate increased to 1.292 ± 0.01 cm·d−1 and 1.285 ± 0.05 cm·d−1, improving by 2.5 g·L−1 LWE and 25 μmol·L−1 MJ, respectively. PUFAs are mainly composed of linoleic acid (LA) and oleic acid (OA). The contents of LA and OA were 0.28 ± 0.02 mg·g−1 and 0.23 ± 0.05 mg·g−1 after MJ treatment, while the contents of LA and OA were 0.08 ± 0.03 mg·g−1 and 0.05 ± 0.05 mg·g−1 after LWE treatment. Transcriptome analyses revealed that 367 and 232 genes within MJ and LWE treatment were significantly different from the basal medium. Out of 13 unigenes, FAD2−2, SCD, and FAD2−1 had the highest expression levels according to the quantitative RT−PCR result. The bioinformatics analysis showed that three genes are closely related to the M8 chromosome of T. camphoratus, and they are hydrophobic transmembrane proteins. The identification and investigation of fatty acid genes in T. camphoratus mycelia will be improved by our findings.