The synthesis of nonnatural phospholipid, phosphatidylhydroxybutyrate (PB), was firstly introduced by phospholipase D (PLD)‐mediated transphosphatidylation of phosphatidylcholine (PC) with sodium γ‐hydroxybutyrate (NaGHB) in the aqueous–solid system. Nanoscale silicon dioxide (NSD) was employed as a carrier to provide an “artificial interphase” between PC and PLD. Special attention has been paid to the effect of the PC coverage on the surface area of hybrids of NSD‐PC, the PC loading and the yield of PB. Results indicated that the highest PC loading of 98.3% and the highest PB yield of 97.3% were achieved. In addition, the free PLD in the aqueous–solid system showed the greater stability and pH tolerance than that in the traditional liquid–liquid system. The operational stability of free PLD solution was investigated. The yield of PB remained 70.7% after being used for five batches. The authors provide a new idea for drug design and the potential source of PB for medical experiments. PB is a potential drug and may have the excellent performance in the treatment of central nervous system's diseases. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2726, 2019