The invention relates to the detection field, in particular to a digestive tract mucosa stain, a preparation method and an application thereof. The digestive tract mucosa staining agent provided by the present invention includes a first dyeing pigment and a second dyeing pigment; the first dyeing pigment includes a blue pigment; and the second dyeing pigment includes a red pigment. When the digestive tract mucous membrane staining agent provided by the present invention is used for staining, it can form a clear contrast with the color of the mucous membrane itself, excellently display the subtle concave-convex changes of the mucous membrane, and display various raised, flat, sunken lesions and their three-dimensional structures, Strong three-dimensional sense, can clearly identify the details in the digestive tract, identify the boundaries of lesions, and significantly improve the detection rate of lesions. In addition, the digestive tract mucosa stain provided by the present invention is very easy to clean, has less residue after washing, and has a clear surgical field, which has good clinical application value.