Enzymatic modification is a green tool for improving starch properties due to its safety, high efficiency, and specificity. Glycosyltransferases, such as 1,4-alpha-glucan branching enzymes and 4,6-alpha-glucanotransferases, offer an effective method to regulate the physicochemical properties of starch, which is referred to as highly-branched modification. It is now emerging as an environmentally friendly starch modification method and deserves a focused and comprehensive review. Herein, we endeavor to present an overview of highly-branched modification and provide insight into its potential advantages compared to other starch modification techniques. For this purpose, we address the critical enzymes used for highly-branched modification, summarize the process of highly-branched modification, detail its effects on the starch characteristics, and outline the potential applications of modified products in the food industry. The highly-branched modification increases the alpha-1,6 glycosidic bond ratio, cyclic glucan content, and short-chain ratio while decreasing the heavy average molecular weight of starch. The resulting products of highly-branched modification showed decreased pasting viscosity, inhibited retrogradation process, improved rheological property, and reduced digestibility. Thus, highly-branched modification has great potential to be used in the starch industry since it effectively creates clean-label starch derivatives with desirable application performance.