The invention discloses a soil DNA indirect extraction method for evaluating the diversity of a plant root system microflora. Because the mean density of bacteria is far smaller than the mean density of soil minerals, a sample is pretreated before cell lysis, and microbial cells are separated from the soil sample, thereby avoiding the problems of difficult humus removal and low DNA recovery rate occurring in the purification process. In the extraction process, the invention does not use phenols or chloroform, the damage to the health of an experimenter is reduced, the obtained DNA is complete, a molecular segment is larger than 10kb, and the yield is high. The OD260/OD230 and the OD260/OD280 of the extracted soil microbe DNA approach to a standard value, and the soil DNA indirect extraction method can be directly applied to molecular operation so as to evaluate the diversity of the plant root system microflora.