Polybenzoxazine (PBa) composites based on phosphorous-containing bio-based furfurylamine type benzoxazines (D-fu) and bisphenol-A type benzoxazines (Ba) were developed for flame retardation. The structure of D-fu was analyzed by Fourier transform infrared (FTIR) spectroscopy and 1H-NMR spectroscopy. The curing temperature of Ba/D-fu mixtures was systematically studied by differential scanning calorimetry (DSC). Thermogravimetric analysis (TGA) demonstrated the excellent char formation ability of the PBa composites with the addition of phosphorous-containing D-fu. The flame retardancy of the PBa composite materials was tested by the limited oxygen index (LOI), vertical burning test (UL-94) and cone calorimeter (CONE). The LOI and UL-94 level of PBa/PD-fu-5% reached 34 and V0 rate, respectively. Notably, the incorporation of 5% D-fu into PBa led to a decrease of 21.9% at the peak of the heat-release rate and a mass-loss reduction of 8.0%. Moreover, the fire performance index increased, which demonstrated that the introduction of D-fu can diminish fire occurrence. The role of D-fu in the condensed and gas phases for the fire-resistant mechanism of the PBa matrix was supported by SEM-EDS and TGA/infrared spectrometry (TG-FTIR), respectively. Dynamic mechanical analysis (DMA) revealed that the Tg of PBa flame-retardant composites was around 230 °C. Therefore, PBa composites are promising fire-retardant polymers that can be applied as high-performance functional materials.