Phylogenomics has greatly deepened our understanding of insect evolution, yet significant gaps remain in certain ancient and fast-evolving lineages. Plecoptera (stoneflies), one of the earliest-diverging groups of winged insects with fossil records dating back to the Carboniferous, remain underrepresented in nuclear genomic studies. Within Plecoptera, the suborder Systellognatha, which accounts for nearly half of extant stonefly diversity, has long presented challenges for phylogenetic resolution due to limited taxon sampling and conflicting signals from different molecular datasets. In this study, we performed low-coverage whole-genome sequencing on 16 Systellognatha specimens from China representing nine genera across five families, including the first-ever nuclear genomic data for the understudied family Styloperlidae. Combined with public transcriptomic datasets, our analysis comprises 68 species and covers all seven families of Systellognatha. Phylogenomic analyses using both site-homogeneous and site-heterogeneous models consistently reject the monophyly of Pteronarcyoidea and identify Styloperlidae as the earliest-diverging lineage within the suborder. Meanwhile, comparative analysis based on molecular systematics and morphology indicates that the number of common derived features during the differentiation process of Pteronarcyidae and Perloidea has decreased sharply. However, Pteronarcyidae exhibits ancestral characteristics. This study not only clarifies key evolutionary relationships within Systellognatha with exceptional certainty but also develops a comprehensive phylogenomic framework that will serve as a resource for future global studies on Plecoptera systematics, biogeography, and early insect evolution in general.