The invention relates to the field of 3D printing mortar, and particularly discloses colored 3D printing mortar and a preparation method thereof, the colored 3D printing mortar comprises the following components: white Portland cement, limestone powder, metakaolin, an organic pigment, an internal curing agent, quartz sand, fibers, a water reducing agent, an alkali-free accelerator, an early strength agent, a defoaming agent, a polymer emulsion and water; the preparation method comprises the following steps: S1, uniformly mixing quartz sand and fibers to obtain M1; S2, uniformly mixing cement, limestone powder, metakaolin, an internal curing agent and M1 to obtain M2; S3, uniformly mixing a water reducing agent, an early strength agent, a defoaming agent and water to obtain M3; S4, uniformly stirring the polymer emulsion and the organic pigment to obtain M4; and S5, uniformly mixing and stirring M3 and M2, adding M4 while stirring, finally adding an accelerator, and uniformly mixing. The prepared mortar is proper in flowability, good in thixotropy and excellent in extrusion performance; and after printing is completed, early strength and later strength are well developed, and the product is bright in color and good in weather resistance.