To solve the problem that photonic crystal (PC) structures constructed by hard nanospheres are easy to be damaged by external forces, resulting in poor durability of the structural colors, polystyrene/poly (methyl methacrylate-butyl acrylate) (PS/P(MMA-BA)) nanospheres were synthesized by means of the step-by-step polymerization method, and the flexible PC films with structural colors were fabricated by using the prepared PS/P(MMA-BA) nanospheres as assembly blocks through melt-shear induced self-assembly method. The results show that the core cross-linking agent, divinylbenzene (DVB), is able to increase the cross-linking density and refractive index of PS core, to produce a certain refractive index contrast with the outer layer, and to make the PS core surface have double bonds, covalently bonding with the outer layer of P(MMA-BA). The outer layer cross-linking agent, allyl methacrylate (ALMA), improves the stability of the outer layer by forming some crossing-linking bonds. When DVB is 12.5% of styrene (St) and ALMA is 0.3% of the total amount of MMA and BA, PC film demonstrates excellent optical and mechanical properties. PC structures assembled by the nanospheres exhibit excellent flexibility, brilliant structural colors, and high stability during the bending, washing and rubbing tests. The melt-shear assembly method adapted to the PS/P(MMA-BA) nanospheres can rapidly fabricate large area of flexible PC film with structural colors.