How to ensure the fire safety of rigid polyurethane (RPU) insulation materials remains a challenge. Herein, alkali lignin (AL) and 4,4'-diphenylmethane diisocyanate (MDI) were used as raw materials to construct bio-based cross-linked polyurethane structures on the surface of ammonium polyphosphate (APP) to obtain APP@AL flame retardants. APP@AL was combined with expandable graphite (EG) in varying proportions and applied to rigid polyurethane (RPU) foam to modify its flame retardancy and physico-mechanical characteristics. Compared with untreated RPU, the high interfacial compatibility increased the compressive strength of the flame-retardant RPUs by 10.8%, and the thermal insulation coefficient reached 22.8mW·m−1·K−1. The addition of flame retardant for each flame-retardant RPU was 30wt% of the polymethylene polyphenyl isocyanate. Owing to the P/C/O hybridized char layer in the combustion residues and the capture of gas by EG after expansion, APP@AL/EG not only reached the limiting oxygen index (LOI) of 27.1% but reduced the mean heat release rate and smoke release rate by 70.3% and 58.9%, respectively. This work presented a novel approach to designing environmentally friendly flame retardants for RPU foams with enhanced fire safety and superior overall performance. Additionally, it offers a novel strategy for the high-value conversion of lignin.