The invention provides a method for evaluating the soil environment safely of transgenic drought-resistant soybeans. The method comprises the following steps: respectively taking 100 g of transgenic drought-resistant soybean root system and 100 g of the same variety of non-transgenic soybean root system for homogenizing and filtering, centrifuging at low temperature by a refrigerated centrifuge 4,000 g, and extracting supernatant to be placed a refrigerator at 4 DEG C for storing and later use; respectively preparing a culture medium suitable for the growths of each functional microorganism and pathogenic microorganism, respectively adding 0, 1%, 0.1%, 0.01%, 0.001% and 0.0001% of the extract of the transgenic drought-resistant soybean root system and the same variety of non-transgenic soybean root system to each selective culture medium and then pouring plate, and repeating for five times; respectively inoculating the functional microorganism such as azotobacteria, silicate bacterium,trichoderma, bacillus megaterium and bacillus subtilis and the soybean root pathogenic bacteria such as phytophthora sojae in each different selective culture medium after pouring plate; after culturing for 5-7 days at 28-30 DEG C, measuring the diameters of the functional microorganisms and the pathogenic microorganisms in each plate culture medium, comparing the significances of differences ofthe diameters of each functional microorganism and each pathogenic microorganism in the culture medium containing the extracts of the transgenic drought-resistant soybean root system and the same variety of non-transgenic soybean root system, and determining whether the transgenic drought-resistant soybean has influence on the soil functional microorganism and the pathogenic microorganism or not.