The invention relates to a natural medicine composition, a preparation method thereof, and an application of the composition in preparation of a toxicity reducing and efficacy enhancing medicine for cancer chemotherapy. The natural medicine composition is composed of a Chinese yam and fructus piperis longi extract after water decoction and concentration, Chinese yam polysaccharide, a fructus piperis longi ethanol extract and piperine in a ratio of (2-6): (3-6): (3-4): (5-9). The composition has an excellent curative effect on diarrhea related with the cancer chemotherapy, and can enhance the effect on the cancer chemotherapy simultaneously.