The purity of nickel-based single crystal alloys plays an important role in the final service performance of turbine blades as it impacts the solidification structure, elemental segregation, and inclusions of castings. The highest purity of superalloys studied before was of altogether around 10 ppm of contents of N and O produced by the triple purification process (VIM+ESR+VAR). However, the impact mechanism still remains controversial, and meanwhile whether a lower content of N and O still keeps the impacts on castings is not yet clear due to the lack of raw materials. A superhigh purity of second generation of nickel-based single crystal superalloy DD98M with the sum of N and O contents as low as 4 ppm (hitherto the highest purity of the superalloy as published), home-produced by electron beam smelting (EBS), was put on focus in this work. The effect of three levels of purity (N-doped, commercial, and EBS, corresponding to 21, 10, and 4 ppm for the sum of N and O contents, respectively) on the microstructure evolution (including primary dendrite arm spacing (PDAS), eutectic, micropores, and γ′ phase) and the solute segregation behavior at dendritic scale and nano scale (γ/γ′ interfaces) were systematically studied and the influencing mechanisms were elucidated. The results show that the PDAS decreased from 406 μm to 322 μm with the reduction of O and N from 21 ppm to 4 ppm, which was irrelevant to precipitation of the nitride or oxide inclusions. Instead, it was due to the decrease of diffusion coefficient D or the increase of equilibrium coefficient k, or the decrease of the critical nucleation supercooling and the incubation time of dendrites. The micro-segregation, the number and volume fraction of eutectic, and the number and voltage percentage of shrinkage pores and gas pores were all greatly decreased with the increase of purity. These changes were closely related to the reduction of PDAS and the reduction of fluidity of the remained liquid in the interdendrites during solidification. The morphology and the size of the γ′ phase were independent from the purity, while the segregation of alloying elements at the γ/γ′ interface changed remarkably with the variation of the purity.