The invention provides a method for extracting DHA from cells of algae and fungi by breaking cell walls and relates to a method for extracting active ingredients from microorganisms. The method provided by the invention avoids the assistance from any organic solvent and chemical medicaments, breaks the walls of the cells of the algae and the fungi by using a physical method and extracts a grease product DHA (docosahexaenoic acid) from the cells and is suitable for large-scale production at low cost. The method comprises: after fermentation is finished, introducing fermentation liquor of microalgae or fungi to a separation system for separating and collecting the cells, adjusting the pH value of bacterial sludge with an acid to 2.0 to 4.0, keeping the temperature of the bacterial sludge between 10 and 20 DEG C, adding antioxidant into the bacterial sludge, and performing high-pressure homogenization and wall breaking by using a high-pressure homogenizer; and adding water into the bacterial sludge subjected to wall breaking, stirring the bacterial sludge, and separating feed liquor in a three-phase separator to obtain DHA grease. In the invention, physical wall breaking and the physical extracting method are used, the process is simple, the cell breaking is high efficient, the low-temperature treatment and antioxidant treatment of the bacterial sludge can effectively protect thebioactivities of the matters in the cells of the algae and the fungi, and the product is green, nontoxic and free from residues.