Glycogen branching enzymes (GBEs, EC 2.4.1.18) play a crucial role in modifying the starch structure and enhancing its properties. The common approaches to starch modification by GBEs typically involve either fully gelatinization the starch at high temperatures (above 95°C) and then cooling it before adding the enzymes or directly modifying the starch granules at medium-low temperatures (below 60°C). However, both of these methods have their limitations. Therefore, in this study, we utilized thermally stable mutant Pyrococcus horikoshii (Ph) OT3 GBEs (The thermally stable Ph GBEs mutant were named as H415W and T508K, respectively) to directly act on an ungelatinized normal corn starch (NCS) emulsion at 70°C, enabling simultaneous starch swelling and branching modification. The results showed that after modification at 70°C, the crystalline structure of the starch almost completely disappeared, the short-branched chains increased, and the amylose content, rapid digestibility, and retrogradation enthalpy (ΔH) of the H415W- and T508K-modified starch were reduced by 8.2%, 20.35%, and 4.38 J/g when compared to the NCS. Furthermore, when compared to wild-type (WT)-modified starch (modification conducted at 60°C), the amylose content, rapid digestibility, and retrogradation enthalpy (ΔH) of the H415W- and T508K-modified starch were reduced by 4%, 11.71% and 1.52 J/g, respectively. The branching efficiency of the starch was enhanced due to the achievement of simultaneous starch swelling and branching modification at 70°C, resulting in an improved branching efficiency. These findings offer valuable insights for the industrial development of branched starch through enzymatic modification.