Based on bio-based furfural, a phosphorus-containing curing agent (FPD) was successfully synthesized, via the addition reaction between 9,10-dihydro-9-oxa-10 phosphaphenanthrene-10-oxide (DOPO) and furfural-derived Schiff base. Then, as co-curing agent, FPD was used to prepare flame retardant epoxy thermosets (EP) cured by 4, 4′-diaminodiphenyl methane. The incorporated FPD improved the flame retardancy and toughness of epoxy thermoset, simultaneously. When 5 wt% FPD was added into EP, the FPD/EP achieved 35.7% limited oxygen index (LOI) value and passed UL94 V-0 rating, meanwhile. In FPD/EP thermoset, the incorporated FPD reduced the thermal decomposition rate, increased the charring capacity, and inhibited the combustion intensity of epoxy thermoset. Through gas-phase and condensed-phase actions in weakening fuel supply, suppressing volatile combustion, and enhancing charring barrier effect, FPD decreased the heat release of burning epoxy thermoset, significantly. For the outstanding effectiveness on both flame retardancy and toughness, the study on FPD provides a promising way to manufacture high-performance epoxy thermoset.