The invention discloses a method for preparing a polyurethane binder for flexible printing composite ink. The method comprises the following steps: preparing a terminal-NCO group prepolymer, namely, mixing polyether glycol, a catalyst and diisocyanate, reacting for 2-4 hours at 50-120 DEG C to obtain a reaction product, namely, the terminal-NCO group prepolymer; and carrying out chain extension synthesis, namely, adding an amine chain extender and an alcohol solvent into an another container to form a mixed solution, feeding the prepared terminal-NCO group prepolymer to the mixed solution within 5-50 minutes and carrying out chain extension reaction for 2-3 hours to obtain polyurethane resin, namely, polyurethane binder for flexible printing composite ink, wherein the reaction temperature is controlled at 30-50 DEG C. The prepared resin has the advantages of good solubleness in alcohol, high cohesive energy, excellent dryness and adhesion force, high composite strength, excellent printability, no foreign smell, no residue, safety and environmental friendliness after printing.