The invention discloses a low-molecular-weight chondroitin sulfate and a preparation method thereof. Macromolecular chondroitin sulfate is used as a raw material, and the low-molecular-weight chondroitin sulfate having average molecular weight of less than 1000 daltons is produced through a production process comprising chondroitin sulfate lyase degradation, deproteinization, filtration sterilization, drying, and the like. According to the low-molecular-weight chondroitin sulfate, the molecular weight distribution range is narrow, the content of chondroitin sulfate disaccharide is 43-60%, thecontent of chondroitin sulfate tetrasaccharide is 30-45%, the sum of contents of the chondroitin sulfate disaccharide and the chondroitin sulfate tetrasaccharide is greater than 87%, the total contentof oligosaccharides in the low-molecular-weight chondroitin sulfate is 97% or above, and the protein content is not more than 0.5%. Compared with common marketed macromolecular chondroitin sulfate, the product has a more obvious repairing effect on chondrocytes damaged by 1mM hydrogen peroxide at a concentration of 50-100 [mu]g/mL, has a strong repairing ability and a repair rate between 14% and23%, can be used to treat joint injuries, and is an important raw material for medical products, healthcare products, cosmetics, food, etc..