Yeast-like symbionts (YLSs), harbored in the abdominal fat body of brown planthoppers (BPHs), Nilaparvata lugens Stål, play an important role in the growth, development, and reproduction of their host. However, little is known about the diversity of the symbiotic fungal YLSs that are harbored in the eggs of BPHs and the difference between fertilized eggs and non-fertilized eggs. Here, we investigate the fungal community compositions of non-fertilized and fertilized eggs of BPHs and identified the YLSs in the hemolymph by qPCR. A total of seven phyla, 126 genera, and 158 species were obtained from all samples, and Ascomycota and Basidiomycota were the most predominant phyla in the non-fertilized and fertilized eggs. The richness index indicated that microbial diversity in the non-fertilized and fertilized eggs exhibited a profound difference. In addition, 11 strains were only identified in the fertilized eggs, and these strains provide new insights into the constitution of species in YLSs. The difference of Pichia guilliermondii in the female hemolymph indicated that fertilization affected the diversity in the eggs by changing the YLSs in the hemolymph. Our research provides a comprehensive understanding of YLS species and their abundance in the eggs of BPHs, and it primarily explores how the changes of YLSs in the hemolymph lead to this difference.