A low molecular weight chondroitin sulfate preparation method relates to chondroitin sulfate. The method includes the steps of stewing sturgeon to remove flesh and fat on the surface of bone, soaking with petroleum ether, washing with ethanol, drying and pulverizing to obtain cartilage particles; adding a NaOH solution to the cartilage particles, stirring for the first time and adjusting the pH to neutral with acid to obtain a cartilage mother solution; adding malic acid to the cartilage mother solution, adjusting the pH to 3.0 to 3.2, adding pepsin, stirring for the second time, adjusting the pH to 5.0 to 5.5, adding papain and cellulase, stirring for the third time, adding activated carbon, stirring for the fourth time and filtering to obtain clarified enzymatic hydrolysate; subjecting the enzymatic hydrolysate to resin adsorption, gradient elution in a NaCl solution, phloroglucinol spectrophotometry detection and combined collection to obtain an eluent with color reaction; precipitating the eluate with ethanol, collecting precipitate through centrifugation and drying to obtain low molecular weight chondroitin sulfate crystals.