Distant hybridization constitutes an important process in plant evolution. Outbreeding of Solanum plants can produce hybrid progeny with heterobeltiosis in terms of growth, development, and resistance. In this study, the genomic characteristics and genetic variation of reciprocal cross F1 hybrids of strains 177 (Solanum melongena L.) and Y11 (Solanum aethiopicum L.) were quantified to analyze the relationship between heterosis and genomic characteristics. While no significant phenotypic differences existed between the F1 hybrids, their phenotypes were closer to those of the Y11 parent. Using whole-genome resequencing, large numbers of single-nucleotide polymorphisms, insertion or deletions, structural variations, and copy number variation (CNV) were found. The variation rate of the Y11 parent was the highest, while those of the F1 hybrids were similar to each other but closer to Y11. These results reflect the fact that the genome of the heterozygous progenies was stable at the chromosome level; nevertheless, a lot of variation sites were produced, which may underlie the increased phenotypic diversities compared to that found in the cultivated parent plants. Mining and functional annotation of variant genes with different variant types revealed that the highest number of variant genes were caused by CNVs. Moreover, the variant genes were significantly enriched in pathways associated with glucose metabolism, protein synthesis, and phytohormone signaling, indicating that CNVs may be responsible for the heterosis observed in the progeny of outbred crosses. These data can provide a reference for future heterosis research, molecular marker development, genetic engineering, high-density linkage map construction, and genome-wide association analysis.