Sperm motility is a critical indicator of semen quality and determines the reproduction performance in male poultry. However, compared to chickens and ducks, very little is known about the physiological basis of varying levels of sperm motility as well the underlying regulatory mechanisms in geese. To address this, in the present study, a systematic comparison of semen quality parameters and histomorphological characteristics and genome-wide transcriptomic profiles of testes and epididymis were performed in ganders with high and low sperm motility. Our results showed that the size, weight, and organ index of bilateral testes and epididymis of ganders from high sperm motility (HSM) group tended to be higher (P > 0.05) than those of ganders from low sperm motility (LSM) group, implying better reproductive organ development in HSM. The ejaculate volume, sperm density, sperm viability, and semen quality factor of the ganders were observed to be significantly higher in HSM than in LSM (P < 0.01), and the opposite was seen in sperm deformity rate (P < 0.01). Moreover, the ganders in HSM showed significantly higher testicular seminiferous epithelial thickness and seminiferous tubule diameter (P < 0.05), higher number of Sertoli cells (SC), spermatids (Sd), and spermatozoa (Sa, P < 0.05), as well as greater diameter and area of epididymal proximal efferent ductule (PED, P < 0.05) than those in LSM. Comparative transcriptomic analysis identified 1,828 and 483 differentially expressed genes (DEGs) in the testis and epididymis of ganders between HSM and LSM, respectively. Functional enrichment analysis revealed that these DEGs were significantly enriched in the Wnt signaling, Apelin signaling, melanogenesis, and GnRH signaling pathways. The protein-protein interaction network analysis further highlighted the hub genes. The testicular DEGs including PLCB1, PLCB2, WNT11, WNT4, and LRP6 were identified to regulate sperm motility through the Wnt signaling pathway, while the epididymal DEGs including WNT3A, WNT9B, SOX2, and SOX10 could affect sperm motility by regulating epididymal cellular proliferation and differentiation. These data provided new insights into the regulatory mechanisms of male poultry reproductive organ development and sperm quality and would be helpful for developing molecular approaches in the genetic improvement of goose fertility.