Bio-based flame retardants have attracted growing attention for sustainability and comparable efficiency to petroleum-based counterparts but suffer from compatibility issues with epoxy resins and the trade-off between strength and toughness. Here, a Schiff base-derived phosphorus-based flame retardant (TV-DOPO) was developed from biobased vanillin and tyramine. In the presence of the binary curing agents, nanoscale in-situ constructive phase separation induced by hierarchical thermal curing process and strong hydrogen bonding provide the composite resin with enhanced both stiffness and toughness. The flexural and impact strengths reached 159 MPa and 55.4 kJ m−2, which were increased by 36.5% and 129.6%, respectively, compared with the pristine epoxy, meanwhile excellent flame retardance was well maintained (UL-94 V-0 rating). Remarkably, these conjugated phosphaphenanthrene-containing composite resins demonstrate excellent UV-shielding capacity and optical transmittance. In this work, in-situ construction of a crosslinked network with tunable size of phase separation domains can be simply achieved by modulating the ratio of binary curing agents, to fabricate epoxy resins with all-around enhanced performance.