Diethyl N,N-bis(2-hydroxyethyl)aminomethyl-phosphonate and halogen-free poly(phosphate) as reactive halogen-free flame retardants and soft or hard segment modifiers were compounded to waterborne polyurethane polyols after being emulsified and then were mixed with isophorone diisocyanate and dimethylolpropionic acid to synthesize two-component waterborne polyurethanes having fire resistance. As a result, the rheological behavior of prepolymer emulsion really accords with characteristics of non-Newtonian fluid. The highest limit oxygen index is 27.8% in two-component system modified by hard segment, which was 527.5% than the clean; meanwhile, one is 28.6% in another two-component system, which was 627.6% than the clean. The hardness, solvent resistance, and mechanical property in both of the two-component systems are outstanding. Adding flame retardant can effectively improve the flame resistance, tensile strength, and pot-life of two-component waterborne polyurethanes, especially in being modified by soft segment.