Chinese bayberry (Myrica rubra or Morella rubra) is a valuable fruit, yet the mechanism of its flesh segment development is not well understood. Using paraffin sectioning, we investigated the flower buds of the ‘Biqi’ and ‘Zaojia’ varieties, revealing that the flesh segment development in these Chinese bayberry varieties involved the formation of a primordium outside the ovary wall, the establishment of a simple columnar structure, and the formation of the primary flesh segment. Assessment of endogenous hormone levels indicated the significant reductions in jasmonic acid (JA) and indole-3-acetic acid (IAA) levels at the critical stages of flesh segment development. Correlation analysis highlighted the essential roles of IAA, JA, abscisic acid (ABA), and gibberellins in the flesh segment developmental process, underscoring the complex interactions driven primarily by the IAA, JA, and ABA networks. Gene modules positively correlated with flesh segment development were identified using transcriptome-based weighted gene co-expression network analysis (WGCNA). Differentially expressed genes (DEGs) were enriched in plant hormone signal transduction pathways, particularly for upregulated genes associated with auxin and JA signaling. Key genes predicted to be involved in flesh segment development included LAX2 and LAX3 (auxin transport), JAZ6 (JA signaling repression), and KAN1 and KAN4 (regulating multiple hormonal signaling pathways). Quantitative real-time polymerase chain reaction (qRT-PCR) validation confirmed that the expression trends for these genes were consistent across both varieties, particularly for CRC, SEP1, SEP3, IAA7, and JAZ6. Immunofluorescence localization studies revealed that auxin was primarily distributed in the central vascular bundle and outer cells of the flesh segment. This uneven auxin distribution might contribute to the unique morphology of flesh segments. Overall, this study provides insights into the hormonal regulation and genetic factors involved in the development of Chinese bayberry flesh segments.