The invention relates to a method for extracting and purifying fucoxanthin from brown alga, which comprises the steps of primary extraction sample preparation, methanol dissolution, column chromatography separation and HPLC (high performance liquid chromatography) purification. The invention provides a fucoxanthin preparation scheme which has the advantages of high safety, low toxicity, high economy and environmental protection. The invention adopts kieselguhr as a column filler to separate the fucoxanthin for the first time. The kieselguhr has the characteristics of low price and environmental protection. Meanwhile, edible petroleum ether is utilized for separation, thereby lowering the residues of toxic substances in the final product. After the kieselguhr is separated, the fucoxanthin health product raw material which is cheap, safe and healthy can be obtained. The fucoxanthin is separated and purified by HPLC to obtain the chromatographically pure fucoxanthin. The invention provides the safe low-toxicity separation technique for satisfying the high-purity fucoxanthin market at home and abroad, greatly enhances the added value of the brown alga aquatic products, and thus, has important economic value.