The solid-state fermentation of Antrodia camphorata could produce a variety of ubiquinone compounds, such as antroquinonol (AQ), AQB, 4-acetyl-AQB and so on. However, ubiquinone compounds are hardly synthesized during liquid-state fermentation (LSF) and the mechanism of synthesis remain unclear. To investigates the influence of different precursors on the synthesis of AQ, three exogenous precursors (ubiquinone 0, UQ0; farnesol and farnesyl diphosphate, FPP) were used in LSF. The results showed that UQ0 successfully induced AQ production; however, farnesol and FPP did not play a role in producing AQ. The results of fermentation experiments show that the precursor that restricts the synthesis of AQ is the quinone ring, not the isoprene side chain. An efficient Agrobacterium-mediated transformation system of A. camphorata was established. Exogenous genes were effectively integrated into the genome of A. camphorata using this system. Then, we overexpressed a series of genes for quinone ring modification (coq2-6) and isoprene synthesis (HMGR, fps) by using the ATMT transformation system, which endogenously increased the content of intracellular precursor for AQ biosynthesis in A. camphorata. The results showed that overexpression of genes for isoprene side chain synthesis could not increase the yield of AQ, but overexpression of coq2 and coq5 could significantly increase AQ production. This is consistent with the results of the fermentation experiment with the addition of precursors. It indicated that the A. camphorata lack the ability to modify the quinone ring of AQ during LSF. Of the modification steps, prenylation of UQ0 is the key step of AQ biosynthesis during LSF. The result will help us to understand the genetic evidence for the requirements of antroquinonol biosynthesis in A. camphorata.