The invention which belongs to bioengineering and bioseparation engineering fields relates to a method for preparing and extracting carotenoid from microbial thalli. The method comprises the following steps: fermenting the microbial thalli, separating the resulting fermentation solution and the thalli to obtain wet thalli, guiding the wet thalli to an explosion tank through a material flow pipeline, and carrying out high-pressure explosion wall breaking; dehydrating the wet thalli with disrupted cells to obtain a filter cake formed by thallium fragments; adding 10-25L of an organic solvent to each 1kg of the filter cake, and carrying out stirring extraction at 30-55DEG C for 20-50min; filtering to obtain an organic solvent extraction containing carotenoid grease; and carrying out vacuum concentration on the extraction at 40-60DEG C, and recovering the organic solvent to obtain the carotenoid grease. The extraction yield one time reaches above 90%. The method has the advantages of omission of dehydration drying and thallium crushing operations in traditional technologies, short process flow, high extraction yield and short time each time, reduced organic solvent application amount, substantially reduced energy consumption and other costs, simple whole process, and controllable quality, and is suitable for industrialized production applications.