The invention relates to a preparation method of the lutein microcapsule with the advantages of simple operation, low costs and high purity. the preparation method comprises the following processing steps of: taking marigold flowers, adding 0.5 to 3 times amount water and 0.005 to 0.1 times amount cellulose, fermenting for 10 to 30 hours under the condition of 30 to 60 DEG C, adding 2 to 30 times amount ethanol, adjusting the PH with NaOH to be alkaline, heating reflux, filtering while hot, adjusting the PH with HCl to be neutral, decompressing and recycling the ethanol, adding the liquid into the macroporous absorption resin column, eluting impurity with water, eluting with 30 to 90% ethanol, collecting eluate, concentrating, adding hexane, methanol, and water with appropriate amount, refrigerating, completely crystallizing, separating the crystallization, washing , drying, grinding, passing 100 mesh sieve, adding modified starch, gelatin and water to make suspension, colloidal milling, and spray drying. The industrialization amplification is easily realized by using the method for preparing the lutein microcapsule.