Structural color materials prepared by lignin colloidal spheres (LCSs) have attracted great interest due to their biocompatibility, biodegradability, multifunctionality, and ability to weaken incoherent scattering. However, the lignin raw materials originating from different biomass resources have distinct heterogeneity leading to a big difference in the size of resultant LCSs via self-assembly, which is a major challenge for the preparation of stable structural colors. In this work, we employ the solvent precipitation method to fractionate the crude lignin samples obtained from corncob, softwood, hardwood, and bamboo, respectively. After solvent precipitation fractionation, the self-assembly behaviors of different lignin samples become similar. The LCSs prepared by fractionated lignin samples show quite similar sizes (212, 202, 215, and 210 nm) compared with the LCSs prepared by crude lignin samples (341, 83, 128, and 253 nm). The quantitative atomic force microscope force spectroscopy demonstrates the improved homogeneity of LCSs prepared by fractionated lignin samples is attributed to similar long-ranged intermolecular forces in self-assembly. By employing LCSs as building blocks, the lignin-based pigments with stable structural colors are successfully prepared. The presented colors are independent of the biomass resource types, which benefits the product stability and large-scale production of lignin-based structural color materials.