Fragrant rhododendron varieties remain relatively limited in current germplasm resources, constraining the enhancement of ornamental and aromatic characteristics in rhododendron breeding—this limitation has emerged as a critical bottleneck in the genetic improvement of rhododendrons. This research takes fragrant flower breeding as the breeding objective and conducts hybridization between varieties of the subgenus Tsutsusi, which can flower in multiple seasons and exhibit relatively strong resistance, and the fragrant R. moulmainense. Parallel intraspecific hybridizations within the subgenus Tsutsusi were implemented as experimental controls to quantify hybridization affinity. This study combines floral tube ontogeny histomorphological analysis, ovary paraffin sectioning, and optimized pollination protocols to address hybridization constraints, providing new insights for rhododendron intersubgeneric distant hybridization to create fragrant varieties. The results showed varying fertility among combinations, with some showing sterility or weak fertility due to low pollen germination and abnormal embryo development. Both pre- and post-fertilization reproductive barriers were observed, and different pollination methods significantly influenced ovary expansion and fruit set rates. Regarding limitations, this study lacks an in-depth analysis of reproductive isolation mechanisms, only describing phenotypic characteristics through morphological and histological methods, and it does not employ molecular techniques. The fundamental causes of reproductive isolation between subgenera therefore remain unclear. Additionally, there was no long-term monitoring of seedling emergence rates, hybrid plant growth potential, or flowering traits. This limits the ability to comprehensively evaluate the breeding value and genetic stability of distant hybrids.