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A rare medicinal fungus called <i>Taiwanofungus camphoratus</i> gives people resistance to illness. In order to effectively obtain high−quality <i>T. camphoratus</i> mycelia, we added <i>Cymbopogon citratus</i> (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 <i>T. camphoratus</i> 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 <i>T. camphoratus</i> 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, <i>FAD2</i>−<i>2</i>, <i>SCD</i>, and <i>FAD2</i>−<i>1</i> 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 <i>T. camphoratus,</i> and they are hydrophobic transmembrane proteins. The identification and investigation of fatty acid genes in <i>T. camphoratus</i> mycelia will be improved by our findings.