Sternorrhyncha, one of the four major suborders of Hemiptera, represents a phytophagous insect clade comprising nearly 18,000 described species. While recent phylogenomic studies have made significant efforts to elucidate the internal phylogenetic relationships within this group, substantial controversies persist regarding both the higher-level phylogeny and particularly the identification of the earliest-diverging lineage. To investigate the phylogenomics of Sternorrhyncha and to reveal the reasons behind phylogenetic conflicts, this study utilizes the available genomic and transcriptomic data to reconstruct the Sternorrhyncha phylogeny and evaluates the impact of alternative evolutionary models on deep-node resolution. A well-supported backbone topology, (Aleyrodoidea, (Psylloidea, (Coccoidea, Aphidoidea))), was consistently recovered across multiple analytical approaches in our study. This study provides critical evidence for resolving the long-standing phylogenetic controversies within this taxon.