The remarkable diversity of the Cyprinidae family highlights the importance of hybridization and gene flow in generating genetic variation, adaptation, and even speciation. However, why do cyprinid fish frequently overcome postzygotic reproductive isolation, a mechanism that normally prevents successful reproduction after fertilization? To address this gap in knowledge, we conducted comparative studies using reciprocal F1 hybrid lineages derived from intergeneric hybridization between the cyprinid species Megalobrama amblycephala and Culter alburnus. Utilizing long-read genome sequencing, ATAC-seq, Hi-C, and mRNA-seq technologies, we identified rapid genomic variations, chromatin remodeling, and gene expression changes in the testicular cells of F1 hybrid individuals. By analyzing the distribution of these alterations across three gene categories (allelic genes, orphan genes, and testis-specific genes), we found that changes were less pronounced in allelic and testis-specific genes but significantly more pronounced in orphan genes. Furthermore, we hypothesize that rnf212b is a crucial testis-specific gene that regulates spermatogenesis. Our findings suggest that allelic and testis-specific genes potentially mitigate "genomic shock" on reproductive function following hybridization. This research offers potential insights into the formation mechanisms of homoploid hybridization by demonstrating the coordinated interplay of genomic variations, chromatin remodeling, and gene expression changes during testicular development and spermatogenesis.