The present invention discloses a method for synchronously separating chloroplast and mitochondria of a high purity plant. The method comprises: A, adding leaf to a CIB buffer liquid, grinding, filtering sequentially with a 70 [mu]m filtration screen, a 35 [mu]m filtration screen and a 15 [mu]m filtration screen, and carrying out centrifugation on the filtrate for 5 min at 200*g to remove tissue residue and cell debris; B, carrying out centrifugation on the filtrate for 10 min at 1000*g, and collecting chloroplast-rich precipitate; C, collecting the supernatant after the centrifugation in the step B, filtering with a 5 [mu] filtration screen, carrying out centrifugation on the filtrate for 10 min at 2000*g, removing the precipitate, carrying out centrifugation on the supernatant for 10 min at 17000*g, and collecting mitochondria-rich precipitate; D, washing the precipitates respectively with a washing buffer liquid, and digesting with DNase I to remove background genome contamination; and E, carrying out centrifugation on the chloroplast precipitate for 10 min at 1000*g, removing the supernatant, carrying out centrifugation on the mitochondrial precipitation for 10 min at 17000*g, removing the supernatant, and washing the precipitates with a washing buffer liquid.