Polypropylene color masterbatches containing modified layered double hydroxides, LDHs, were created. The simple, industry-acceptable method of LDH surface modification with quinacridone and phthalocyanine pigments using the pulverization method in ball mills was applied. It was reported that the modification parameters such as time and rotational speed affected the tendency to create the aggregates for modified fillers. TGA analysis of the modified LDH showed that modification with phthalocyanine pigment shifted the temperature at which 5%, T5%, and 10% of mass loss, T10%, occurred compared with that for unmodified LDH. The viscoelastic properties of prepared masterbatches were investigated. The incorporation of the modified fillers instead of neat pigments led to an increase in the loss shear modulus, G″, indicating a stronger influence on the dissipation of energy by the melted masterbatch. The similar values of tan, δ, were determined for melted masterbatches containing phthalocyanine pigment and green modified LDH filler. The incorporation of both LDHs modified by phthalocyanine and quinacridone pigment fillers slightly increased the zero-shear viscosity, η0, compared with that of the masterbatches based on the neat pigments. The Cole–Cole plots and the analysis of the Maxwell and continuous relaxation models showed that modified colored LDH fillers facilitated the relaxation of the melted masterbatch, and shorter relaxation times were observed. The phthalocyanine-modified LDH filler improved the thermal stability of the masterbatches. Additionally, the impact of pigments and modified, colored LDH on the crystallization of polypropylene was investigated.