We have developed a companion-planted grow seedlings technique, based on the plastic hole plate method used for large-scale crop seedling production, for growing gramineous crops in combination with target crops such as cotton, rape, tomato, and peanut in the same planting hole. This new grow seedlings method takes advantage of the fibrous root system of gramineous crops to keep the root system of growing seedlings tightly bound together, thus preventing damage to seedling root systems during removal from plastic hole trays and mechanical transplantation into the field. Because of its superior suitability for mechanical transplantation, the technique increases the survival percentage of transplanted seedlings, shortens the post-transplantation convalescence period, and improves target crop quality. To elucidate the mechanisms responsible for enhancing crop seedling quality when two crops are grown in the same hole, we studied the eco-physiological effects of the new technique on soil microorganism quantity, enzyme activity, and root secretion, as well as target crop root vigor and soluble sugar and adenosine triphosphate leaf content. Wheat, maize, millet, and sorghum were used to promote seedling growth of target crops such as cotton, rape, tomato, peanut, peony, and tobacco. Seeds were sown in 532×280 mm² plastic trays containing 200 square holes with soil as a substrate, and the resulting seedlings were grown under natural light conditions at 20-30℃ in plastic sheds. When crop seedlings were companion-grown in this fashion, the number of bacteria and actinomycetes in the matrix soil increased significantly-by 52.80%-102.76% and 34.11%-76.48%, respectively-and the number of fungi in the soil decreased by 44.33%-56.14%. Soil enzyme activity also increased significantly; for example, increased activity was observed for dehydrogenase (30.57%-66.37%), neutral phosphatase (38.17%-54.37%), invertase (23.74%-35.04%), and urease (60.25%-85.47%). At the same time, significant decreases were detected in root exudates, including 2,4-di-tert-butylphenol (32.80%-51.65%), 2,6-di-tert-butylphenol (36.60%-56.59%), dibutyl phthalate (10.42%-49.99%), and methyl palmitoleate (25.62%-55.59%). Root vigor and soluble sugar and adenosine triphosphate content in leaves of target crops increased significantly. As a consequence, root weight, seedling weight, and lateral roots of target crops increased; these results revealed robust growth, strong photosynthetic capacity, and greater reserve power, which laid the material and energy foundation for quick regrowth and enhanced survival of transplanted seedlings. Among treatments, the most favorable results were obtained for cotton-wheat, cotton-millet, rape-millet, tomato-wheat, tomato-millet, peanut-wheat, peanut-millet, peony-millet, and tobacco-millet combinations. In conclusion, the quantity and colony composition of soil microorganisms was improved when two seedlings of two crops were companion-planted in the same hole. This soil microorganism enhancement may have been the primary cause of increased soil enzyme activity and decreased accumulation of detrimental root exudates; it would help reduce crop auto-toxicity and improve soil nutritional conditions, thus boosting target crop seedling quality. Soil microorganisms play an important role in soil nutrition transformation, organic matter decomposition, detrimental material degradation, and soil fertility recovery. In addition, they can produce growth stimulants and antibiotics, which stimulate crop growth and suppress growth of harmful microorganisms, respectively. The improved soil microorganism composition and increased soil enzyme activity observed when seedlings of two crops were companion-planted may be related to additive effects of root system exudates from the two crops; both crop type and nutritional situation may affect the quantity and type of these secretions, which enhance soil microbe quantity and soil enzyme activity.