Abstract: A research method using molecular docking technique as a guide for screening the wall material of the microcapsules of mulberry red pigment was developed. Docking scores and hydrogen bonds strength were used to evaluate the binding ability between given candidate proteins and cyanidin 3-O- (6″-O-α-rhamnosyl-β-galactoside), the major component present in mulberry. The verification experiments about the suitability of the screened protein as wall material for mulberry red pigment microcapsules were carried out subsequently. The results were as follows: soybean protein (basic 7S globulin and H-2 ferritin) shows stronger binding capability to cyanidin-3-O- (6″-O-α-rhamnosyl-β-galactoside) than egg protein (uncleaved ovalbumin & S-ovalbumin) and milk protein (α-Lactalbumin & β-lactoglobulin); the inclusion rate of mulberry red pigment increases with the increase of the proportion of soy protein isolate in the wall materials mixture composed of soybean protein isolate and β-cyclodextrin. The optimized parameters for mulberry red pigment microcapsules are 8∶2 for the mass ratio of soybean protein isolate and β-cyclodextrin and 1∶10 for core-to-wall ratio. Complete inclusion structures with 500 nm or 250 nm resolution were revealed in the micrograph of mulberry red pigment microcapsules prepared according to above parameters, and higher stability of mulberry red pigment in those microcapsules was observed comparing to the control. It could be indicated that the method of molecular docking has application potential in the study of microcapsules and similar situations.