Pitaya is renowned for its delicious taste, high nutritional value, and economic as well as ornamental appeal. Breeding new pitaya varieties can boost economic returns by appealing to consumers with diverse morphological traits. However, the genetic basis underlying key traits in intergeneric hybrids of pitaya has yet to be fully understood. This study investigates the genetic dynamics in flower, fruit, and stem traits, including segregation patterns and a mixed inheritance model for major and polygenic traits, in an intergeneric hybridization between 'Honghuagqinglong' (HHQL) () and 'Heilong' (HL) (). The study identified normal or skewed, normal distribution patterns in seven floral, fifteen fruit, and five stem traits, indicating their quantitative nature governed by multiple genes. Specifically, flower size and color exhibited a hereditary bias towards 'HL' characteristics, while 'HHQL' significantly influenced the coloration of fruit peel and pulp. Fruit weight and total soluble solids (TSS) content decreased, whereas stem traits exhibited broader and thicker dimensions with fewer thorns. This study offers valuable insights into genetic variation and the influence of major genes on flower, fruit, and stem traits between 'HHQL' and 'HL' intergeneric hybrids, providing a useful reference for parental selection in pitaya breeding programs.