Phosphatidylserine (PS) is a natural phospholipid with particular importance in the food, cosmetic, and pharmaceutical industries. Recently, the synthesis of PS mediated by phospholipase D (PLD) has drawn great attention. But the application of free PLD is limited by various drawbacks, including its instability under extreme conditions, difficulties in reuse and recovery, and high costs. In this work, saPLD-inorganic hybrid nanoflowers (saPLD@NFs) were synthesized with PLD from Streptomyces antibioticus (saPLD) as the organic component and Ca3(PO4)2 as the inorganic component. The saPLD@NFs demonstrated outstanding immobilization capability and achieved a 119% enzyme activity recovery rate. Furthermore, the saPLD@NFs exhibited better thermostability and pH stability in comparison to free saPLD. The PS yield of saPLD@NFs was about 57.4% in the first cycles and still reached 60.4% of its initial PS yield after four cycles. After 25 d storage at 4 °C, saPLD@NFs retained 66.5% of its original activity, but free saPLD only retained 38.3%, indicating that saPLD@NFs have excellent storage stability. Thus, this study established a new method of preparing PLD nanoflowers for effective PS synthesis, which might accelerate the practical utilization of this biocatalyst.