In this study, three cold soybean varieties, namely Kangxian-9, Kangxian-13, and Fudou-6, were used for the high-throughput calculation of soybean plant heights. Three varieties were used to overcome the disadvantages of the traditional measurement methods, which were inefficient and laborious. The method for calculating the plant heights of individual and grouped soybean plants was proposed using the depth information acquired from the three-dimensional reconstruction of soybean canopies obtained using the Kinect V2.0 synchronous image acquisition platform. The experimental results show that compared with the measured value, the average errors of the proposed calculation method for the plant heights of individual and grouped soybean plants are 0.14 cm and 0.54 cm, respectively. The determination coefficients between calculated and measured values for Kangxian-9, Kangxian-13, and Fudou-6 are 0.9717, 0.9730, and 0.9697, respectively. Thus, the proposed method can accurately calculate the heights of soybean plants.