The invention discloses recombinant pichia pastoris (GS115-ppic9-novQ) preserved in CCTCC (China center for type culture collection) on March 11, 2016 with the preservation number of CCTCC M 2016105. The invention further discloses a construction method of the recombinant pichia pastoris and an application in production of aromatic prenyltransferase. By means of induction culture of the engineering bacterium, soluble recombinant aromatic prenyltransferase NovQ with biological activity can be directly obtained in supernatant of a fermentation liquid, and processes such as cell collection, cell disruption and the like are omitted, accordingly, the production process is simplified. Compared with enzymes from other sources, the aromatic prenyltransferase has the advantages that the activity does not depend on structures such as a living cell or a biological membrane, the substrate specificity is low, prenylation of multiple substrates can be catalyzed, the catalytic activity is high and the like.