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Soybean is an important grain and oil crop and is widely cultivated worldwide. As a plant growth regulator, mepiquat chloride (DPC) has the effect of regulating plant type and is widely used in cotton planting, but there are few studies in soybean. In this study, the regulation of DPC on soybean was explored by morphology, physiology and proteomics. The results of morphological and physiological experiments showed that DPC significantly reduced the plant height and shoot dry weight of soybean, promoted the growth of lateral roots in a certain concentration range, increased the activities of leaf protective enzymes superoxide dismutase (SOD) and catalase (POD), decreased the content of malondialdehyde (MDA), and increased the content of total flavonoids. Proteomic analysis of soybean leaves treated with 100 mg/L DPC showed that multiple proteins related to plant growth and stress resistance were regulated after treatment. The key proteins involved in photosynthesis and cell wall elongation of the two varieties of soybean were significantly down-regulated, and the proteins related to promoting lateral root growth and stress resistance were significantly up-regulated. In summary, DPC inhibited the shoot growth and photosynthesis of soybean, but promoted the lateral root growth, enhanced the protective enzyme activity, and helped to improve the ability of plants to resist abiotic stress. This study preliminarily screened out the suitable DPC concentration for soybean spraying, and provided a theoretical basis for its rational application in soybean.