The invention relates to a method for extracting a DNA of an algae chloroplast. The method comprises the following steps of carrying out pulp homogenization of fresh or frozen algae as a raw material by a tissue pulp homogenization machine, adding a buffer solution A into the homogenate obtained by the previous step, carrying out centrifugation by a centrifugal force of 3000 to 6000xg, collecting precipitates, adding a buffer solution B into the precipitates, carrying out water bath pyrolysis at a temperature of 60 to 70 DEG C for 1 to 2 hours, removing denatured proteins of the lysate, adding CsCl and Hoechst 33258 into the lysate, carrying out centrifugation by a centrifugal force of 36000 to 40000xg for 8 to 12 hours, taking out a stripe containing a DNA of an algae chloroplast, removing Hoechst 33258, adding 2.5 to 3.5M of sodium acetate, double distilled water and isopropanol into the stripe, standing at a temperature of -20 DEG C for 20 to 40 minutes, carrying out centrifugation by a centrifugal force of 12000 to 16000xg for 15 to 30 minutes to obtain precipitates, and carrying out purification to obtain the DNA of the algae chloroplast. Compared with the prior art, the method simplifies extraction processes, has simple and feasible processes, improves an extraction ratio and purity of a DNA of an algae chloroplast, realizes an algae (fresh algae) chloroplast DNA yield of 150 to 200 micrograms per gram, and can fully satisfy requirements of conventional molecular biology processes such as genomic sequencing, specific enzyme digestion, random amplified polymorphic DNA (RAPD), polymerase chain reaction (PCR) and target gene sequence cloning.