Abstract: This disclosure presents a composition for tissue staining and 3D specimen optical clearing, along with a method of making biological material transparent and labeling it simultaneously. The composition includes an amide dye adjuvant, a RI-matching material, a permeating agent, a labeling material, a mixture homogeneity excipient, and a solvent with DMSO. The RI-matching material includes a contrast agent and sugar. The composition has a neutral or acidic pH. The method involves fixing a specimen with a fixative solution and immersing and incubating the specimen in the composition for permeation. This disclosure also presents a kit for rendering biological material transparent. The kit is helpful for experimental animal/human histological studies and cancer staging/tumor differentiation determination.