Papaya is a trioecious species, but a unified framework for comparing floral sex differentiation has been lacking. We combined stereomicroscopy, paraffin sectioning, and scanning electron microscopy to establish a continuous 12-stage developmental system from floral primordium initiation to anthesis. Male, female, and hermaphroditic flowers followed a common developmental trajectory during Stages 1–4 and diverged at Stage 5. Male flowers formed fertile stamens and a reduced pistillode, female flowers developed a complete gynoecium without stamens, and hermaphroditic flowers displayed normal, aborted, or transitional pistils and carpellodic stamens. RNA sequencing and weighted gene co-expression network analysis of morphologically defined tissues identified gene modules associated with normal pistil development, distinct modes of pistil abortion, and stamen carpellody. These modules were enriched in chromatin and RNA regulation, protein homeostasis, floral-organ identity, hormone and receptor-kinase signaling, pollen-wall formation, and stress-responsive pathways, yielding 30 representative candidate genes. This developmental framework integrates developmental morphology with transcriptional programs underlying reproductive-organ fate and plasticity in papaya.