<p>The mitochondrial and nuclear genomes present distinct inheritance and genomic structural characteristics. Although both genomes have been widely used for phylogenetic tree reconstruction, topological discordances between trees inferred from mitochondrial and nuclear genomes—referred to as mito-nuclear phylogenetic discordance—have been widely reported. In this study, we analyzed the mitochondrial and nuclear genomic data from 472 insects and systematically investigated the impact of gene properties on the mito-nuclear phylogenetic tree discordance. Our analyses revealed that this discordance was not attributed to most examined factors, such as gene length and gene tree resolution, with the exception of guanine-cytosine content (GC%). We found that the mitochondrial genes exhibited significantly lower GC% compared to the nuclear genes. Further analyses revealed that the mito-nuclear phylogenetic discordance can be reduced by sampling mito-like nuclear genes that possess a similar GC content to that of mitochondrial genes. Moreover, we found that within nuclear genomes, low-GC nuclear genes are more topologically similar to each other and exhibit different biological functions than high-GC nuclear genes. These findings enhance our understanding of the mito-nuclear phylogenetic tree discordance in insects.</p>