ABSTRACT The Characiformes exhibit remarkable dietary diversity, with carnivorous species displaying unique adaptations to high‐protein and high‐fat diets. However, the molecular mechanisms underlying this carnivorous specialization remain poorly understood. In this study, we adopted comparative genomic approaches using 12 high‐quality Characiformes genomes (covering nine subfamilies) with zebrafish as an outgroup. We first re‐annotated the genomes of five Characiformes species, subsequently performing phylogenetic reconstruction, gene family expansion and contraction analysis, candidate gene identification, and amino acid site substitution analyses. Enrichment analysis revealed that expanded gene families, positively selected genes, and rapidly evolving genes in Characiformes were predominantly linked to amino acid metabolism, lipid absorption and transport, energy metabolism regulation, and chitin‐related. Furthermore, amino acid substitutions in phospho1 and hsd17b7 were found to lead to substantial alterations in protein 3D structures, potentially modifying their biological functions associated with lipid metabolic homeostasis. These candidate genes are hypothesized to facilitate the efficient absorption and utilization of high‐protein and high‐fat diets by carnivorous Characiformes while mitigating adverse effects. Our findings reveal the molecular basis of carnivorous adaptation in Characiformes, providing a foundation for future functional validation and novel insights into dietary diversification in teleost fish.