Method of manufacturing gradient composite material comprises steps of providing plural surface modified inorganic nanoparticles with functional groups or oligomers with functional groups; transferring the surface modified inorganic nanoparticles or oligomers with functional groups into an organic matrix to form a mixture; performing a photo polymerization step or a thermo-polymerization step for polymerizing and generating a gradient distribution of the surface modified inorganic nanoparticles or oligomers with functional groups in the mixture; and curing the mixture to solidify the organic matrix and form a structure with gradient composite, wherein the organic matrix is transferred into an organic polymer after curing.