Increase in branching boosts soybean yield but often causes delayed flowering, thereby limiting its application in high-latitude regions with short frost-free periods. Here, through positional cloning, we identify a branching-regulating gene on chromosome 6 (TOO MANY SHOOT BRANCHING 6, TMS6), which represses branching but does not affect the flowering time and maturity in soybean. Functional analysis reveals that TMS6 associates with and activates the promoters of cytokinin oxidases, consequently reducing cytokinin levels in axillary buds and resulting in fewer branches. Geographic distribution analysis reveals that the frequency of the low-branching TMS6 allele decreases from higher latitudes to lower latitudes, consistent with the branch number change pattern. TMS6 mutations boost individual plant grain yield. Introgression of tms6 alleles into an elite cultivar originating from a high-latitude region increases plot yield in field trials. This study provides a soybean branching-regulating gene as a potential target to improve yield in high-latitude regions.