The as-cast structure of high-alloyed wrought superalloys exhibits disadvantages such as high microscopic segregation and poor microstructure uniformity, severely affecting their subsequent hot working and deformation properties. To optimize the as-cast structure of the wrought superalloy, GH4068 alloy was smelted via electron beam smelting (EBS), and its ingots with low segregation were prepared by setting different EBS powers for 10 min. The results show that the bottom of the ingots after EBS appeared to be fine grain regions, with the presence of only cellular segregation structure and cellular dendritic crystal; the large area in the middle became vertically growing columnar crystal regions, the direction of secondary dendrite crystal growth was parallel to that of the columnar crystal growth; a small amount of equiaxed crystal was observed at the top, and the growth direction of dendritic crystals was disordered. Analyzing the compositions of ingots revealed that Cr volatilization in this alloy was the most obvious; the Cr content decreased by 1.97% when the EBS power was 17 kW. The ingot structure prepared via EBS was more highly distributed than that obtained using the traditional vacuum induction melting + electroslag remelting duplex process. When the EBS power was 12 kW, the secondary dendrite spacing λ₂ was 44.6 μm, which was 32.2% less than that yielded using the duplex process, the degree of the microscopic segregation of the ingot dendrite region decreased considerably, and the degree of the microscopic segregation of the typical easily segregated elements Ti and W reduced by 20.4% and 18.6%, respectively. Furthermore, the massive precipitation of large interdendritic γ′ phases were observed, while the γ′ phases in the dendritic core were spherical and smaller in size than those in the interdendritic. Meanwhile, the ingot prepared with an EBS power of 12 kW achieved the smallest size for γ′ phases and least irregular γ′ phases in the interdendritic. In the EBS process, the actual melt temperature was considerably higher than the alloy melting temperature. After the overheating of the melt, the cluster structure effectively decomposed, elements were uniformly distributed, the degree of subcooling increased in the solidification process, and the uniformity of the melt was inherited to the solidification structure to refine the as-cast structure and reduce the degree of microscopic segregation. Meanwhile, during the EBS process, local high temperature generated due to the electron beam bombardment on the surface of the molten pool effectively reduced the N content in the alloy.