The invention belongs to the technical field of extraction and discloses a method for extracting a natural red pigment from pitaya and application thereof. The method comprises the following steps: (1) selecting fresh red pitaya, peeling off, dicing and crushing flesh to obtain fruit pulp, and then refrigerating the fruit pulp; (2) taking out the refrigerated fruit pulp in the step (1) and unfreezing at the room temperature, then adding distilled water and pectinase and uniformly stirring, and extracting at 20-35 DEG C for 0.5h-2h; (3) filtering an extracting solution extracted in the step (2), and centrifuging the obtained filtrate to obtain a clarified pigment solution; and (4) mixing the clarified pigment solution obtained by the step (3) with wall materials, stirring at the room temperature for completely and uniformly mixing, and drying to obtain a dry pigment product. The method has the advantages of simplicity in operation, high efficiency and energy saving, environmental friendliness and capability of keeping natural active components in the pitaya to the greatest extent; the weight of freeze-dried products is light and the quality is good; the products can be stored for a long time and are convenient to transport; and the obtained pigment solution can be directly applied to food production.