As root exudates play an important role in mobilization of soil nutrients and mitigation of environmental stress, many scientists show great interests in root exudates, and have achieved some progresses in the research of those substances. However, it is still not an easy job to collect root exudates from plants growing in soil. Here, a new type of device and method is introduced for collecting root exudates from plants growing in soil. The device consists of a culture box and a collection box. During growth the plant in the culture box, affected by the oriented guidance technique, extends its roots through the agar medium into the collection box. When a certain amount of plant roots develop in the collection box, the medium in the box is leached for collection of root exudates. In this experiment, soybean was planted and cultured for 3 weeks. By then, more than 90% of the total root tips and 30% of the total root biomass were distributed in the collection box. In-situ recovery rate of organic acids reached over 70% in this system, it was found that secretion of organic acids from the roots of soybean under soil culture increased with its growth period. Soybean roots secreted more malate than citrate. Secretion of citrate and malate under soil culture were 11.4 and 6.7 times as much as under solution culture, respectively. The above findings suggest that this device is applicable to collecting organic acids secreted from plant roots under soil culture.