Ammonium polyphosphate (APP) and self-made nickel phytate (PANi) were used as modified materials to prepare green biomass rigid polyurethane foam (RPUF). The flame retardancy, thermal stability, smoke toxicity and mechanical properties of the modified RPUF were investigated by limiting oxygen index (LOI), a cone calorimetry (CONE) test, thermogravimetric analysis and a compression test. The results showed that the RPUF with 10 wt% APP (PANi/APP10) had the highest LOI of 26.5%. Its peak heat release rate (PHRR) and total heat release (THR) were reduced by 29.64% and 24.05% compared with PANi/APP0 without APP. And its smoke production rate (SPR) and total smoke release (TSR) decreased by 33.14% and 19.88%, respectively. Compared with pure RPUF, the compressive strength of PANi/APP10 was increased by 50%, mainly because APP itself was an ultra-fine powder, which was better compatible with the matrix and improved the hardness of the material. The results showed that the synergistic effect of the gas phase and the condensed phase mechanism could effectively improve the flame-retardant effect. The current research results provided a new strategy for the preparation of green and low-toxicity RPUF.