A novel phosphorus-silicon flame retardant (P5PSQ) was prepared by bonding phosphate to silicon-based polysilsesquioxane (PSQ) and used as flame retardant of poly (lactic acid) (PLA). The results show that PLA with 10 wt % P5PSQ has a limiting oxygen index (LOI) 24.1%, the peak heat release rate (PHRR) and total heat release (THR) of PLA decrease 21.8% and 25.2% compared to neat PLA in cone calorimetric test, indicating that P5PSQ shows better flame retardancy in comparison to PSQ. Furthermore, the study for the morphology and composition of carbon residue after the combustion of PLA and the gas release of PLA during combustion illustrate that P5PSQ has flame retardancy in condensed phase and gas phase simultaneously. In condensed phase, phosphorus from phosphate promotes the formation of more stable and better carbon layer containing Si and P, which inhibits the transfer of heat and oxygen in the combustion. In gas phase, the phosphate in P5PSQ emits phosphorus-containing compound that can restrain the release of C–O containing products, which may have effective flame retardancy for PLA in gas phase to a certain extent. In one word, P5PSQ is denoted as a good phosphorus-silicon synergistic flame-retardant.