Trace elements such as boron (B) and zirconium (Zr) can increase creep resistance in nickel-based superalloys. This study investigates the change of microstructures on the grain boundary (GB) in phase-controlled nickel-based superalloys through the addition of trace elements. The basis alloy without B and Zr has distributed micrometer-sized (Nb, Ti)C and Cr23C6 carbides at the GBs. Zr is detected alongside Nb and Ti within certain (Nb, Ti)C carbides and its addition increases the fraction of (Nb, Ti)C or (Nb, Ti, Zr)C carbides. B affects the formation of precipitates constructed by nanometer-sized precipitates, which are Cr23C6 carbides, Cr23(C, B)6 boro-carbides, and Cr-rich borides, surrounded by γ’ phases. This film structure, which includes nanometer-sized precipitates surrounded by γ’ phases, forms more continuously with the addition of B and Zr. It is constructed with precipitates of (Nb, Ti)C carbides and Cr23(C, B)6 boro-carbides surrounded by γ’ phases. Numerous nanometer-sized precipitates (i.e., (Nb, Ti)C and Cr23(C, B)6) are distributed alternately within the film structure. The effect of the addition of B and Zr is such that nucleation sites of each precipitate are formed simultaneously and alternately along the GBs. The experimental results were discussed by correlating them with the predicted fraction of stable phases depending on the temperatures of these alloys, using the JMatPro program.