<p>The behaviour of B chromosomes—supernumerary chromosomes found across diverse organisms—during meiosis and genetic effects in lilies is poorly understood. Here, we systematically investigated the behaviour of the B chromosome of triploid lily ‘Orange Emperor’ during meiosis via conventional cytological techniques, focusing on its dynamics across meiotic stages, its influence on genetic diversity, and interactions with A chromosomes. Furthermore, we used ‘Orange Emperor’ as a maternal parent in hybridisation with Asiatic lilies to analyse progeny genetic characteristics. The results indicate that the B chromosome in ‘Orange Emperor’ remains univalent and does not associate with any A chromosome during meiosis. Separation primarily occurs at anaphase I, followed by random distribution in the resulting microspores. A cross between ‘Orange Emperor’ (female parent) and a diploid Asiatic lily yielded few offspring. All hybrid progeny were aneuploids with variable number of A chromosome (ranging from 25 to 31) and, in some cases, contained at most one B chromosome as a supernumerary element. We found unique meiotic behaviour and inheritance patterns of B chromosomes. The B chromosome exhibited lack of pairing and precocious separation in male meiosis, followed by random distribution in microspores. When transmitted through female lineage, a single B chromosome copy was inherited by ~ 50% of hybrid progeny. These observations are consistent with a model of random segregation during female meiosis coupled with strong post-meiotic selection against gametes or zygotes carrying multiple B chromosomes. This study provides a cytogenetic foundation for understanding how B chromosome copy number is regulated in polyploid backgrounds.</p>