Seedless is a highly valued commercial characteristic in the citrus industry, both for fresh consumption and for processed markets. In this study, the ‘Succari Sweet Orange’ (WT) and its seedless mutant ‘Juxiangyuan’ (MT), which originated from a bud mutation, were selected to study the formation of a citrus seedless phenotype. Microscopic analysis of MT’s floral organs, including anther and ovary cross-sections, provides insights into its seedless phenotype compared to the original seeded cultivar. Additionally, pollen features, viability, and in vitro germination were examined to determine the cause of seedlessness. MT exhibited significant developmental deformities in both male and female gametes, with pollen grain analysis indicating a high rate of deformity (41.48%), low viability (9.59%), and minimal in vitro germination (9.56%). Hybridization experiments were conducted to assess male and female sterility and pollen incompatibility. Both WT and MT exhibited parthenocarpic development. Notably, MT fruit produced with an average of 3.51 seeds pollinated to WT, despite severe pollen abortion of MT. MT, however, produced seedless fruit through self-breeding or cross-breeding with other varieties, demonstrating stable female sterility. Despite reduced pollen quantity and viability in the seedless mutant ‘Juxiangyuan’, its seedlessness primarily stems from female sterility. This study contributed to a deeper understanding of seedless formation in ‘Juxiangyuan’ and provided valuable information relevant to its commercial cultivation.