The invention relates to a concrete penetrating coloring agent and application thereof. The concrete penetrating coloring agent is prepared from the following components of organic pigment, a solvent,a penetrant, a wetting agent, an emulsifier, a silane coupling agent and a thinner. The concrete penetrating coloring agent has the advantages that the penetrating property is strong, the coloring agent can effectively penetrate into a concrete surface layer and generate chemical reaction with a concrete substrate, and a colorful concrete whole structure with stable color can be formed; the operation is simple, the convenience in use is realized, the colorful effect is realized, more than twenty conventional colors can be formed, and the required other colors can be blended by the existing colors; the conventional colors include golden yellow color, orange yellow color, camel color, brown color, coffee color, orange red color, claret color, bright red color, garnet color, purple color, bright green color, jade green color, dark green color, water gray blue color, bright blue color, peacock blue color, deep blue color, light gray color, medium gray color, pure black color and the like,and every two colors or more colors can be mixed to form other colors.