The invention relates to a preparation method of environment-friendly nanometer water-based color paste, which comprises the following steps: 1) uniformly mixing pigment, a surfactant and a solvent toobtain a mixed solution A; 2) adding a grinding medium into the mixed solution A to obtain a blend, and performing dispersing and grinding; 3) performing grinding medium separation and filtration onthe dispersed and ground blend to obtain a mixed solution B; 4) performing grain size screening and filtration on the mixed solution B to obtain the water-based color paste which has small color pastegrain size, uniform grain size distribution, high environmental protection level and stable state.