The invention discloses a method for extracting mitochondrial deoxyribonucleic acid (DNA) of cotton. The method comprises the following steps of: (1) homogenizing cotton, and centrifuging and collecting precipitate; (2) removing nuclear DNA, adding ethylene diamine tetraacetic acid (EDTA) solution, and centrifuging to obtain the precipitate; (3) adding buffer solution, and centrifuging to obtain mitochondria; (4) adding lysis solution and acetate solution, centrifuging, collecting supernatant, and extracting by using chloroform-isoamylol; (5) adding acetate solution and absolute ethanol, centrifuging to obtain the precipitate, and washing by using ethanol; (6) dissolving in triisopropylphenylsulfonyl (Tris)-EDTA (TE); (7) removing ribonucleic acid (RNA) and protein, extracting by using Tris saturated phenol-chloroform-isoamylol, and centrifuging and collecting the supernatant; and (8) adding the acetate solution and the ethanol, and centrifuging to obtain the precipitate; and washing by using the ethanol to obtain the mitochondrial DNA. Aiming at defects of the conventional extraction of the mitochondrial DNA, the conventional cetyltrimethylammonium bromide (CTAB) method is improved, and the extraction conditions are optimized by adjusting the time and times of centrifugation, changing reagents, increasing extraction and washing times, and the like. On the basis of ensuring that the mechanical damage degree of the mitochondria is minimum, the nuclear DNA, phenols and polysaccharides outside the mitochondria are effectively removed, pollution rate is reduced, the purity and the quality of the mitochondrial DNA are improved, and the mitochondrial DNA can meet the requirement of subsequent experiments of the gene engineering of the cotton mitochondria.