The Chinese citrus fly, Bactrocera minax (Enderlein) (Diptera: Tephritidae), is an important pest of citrus crops. In this paper, morphological characteristics of the male external genitalia, the length of the aedeagus, the length from the female cloaca to the spermatheca, as well as the clamping characteristics of the male and female, the male's distiphallus reaching the position of the female's vagina during mating of B. minax, were observed and measured on optical microscopy, scanning electron microscopy (SEM) and three-dimensional X-ray microscopy (X-ray CT). The results showed that the male genitalia of B. minax was composed of aedeagus (phallus and distiphallus), genital apodeme (fultella and genital ring) and clasper (surstylus and claspette). The phallus was a long and curved double-pipe structure (bending to the ventral surface), the outer tube was the phallus and contained an ejaculatory duct (inner tube). The phallus had a low degree of sclerotization due to its fold on the abdomen, and the back was flat (with a groove in the middle), with a high degree of sclerotization, which can be both bent, folded and straightened. When the male rested, the aedeagus curled up, most of which was hidden in the fifth abdominal segment. The distiphallus was composed of the genital rod and the distiphallus body (basal sac, trumpet, split and sclerotization area). The sperm outlet was located inside the trumpet at the top of the distiphallus and the split on the distiphallus body at the anterior end of the basal sac. During mating, the male clasper clamped the distal part of tergite of the female oviposition needle, and the farthest distance that the aedeagus reached through the cloaca was the female bursa copulatrix. The length from the cloacal opening to the spermatheca of female adult B. minax (21.64 ± 0.59 mm) was much longer than that of aedeagus of male adult (9.21 ± 0.25 mm), which indicated that male aedeagus could not reach the spermatheca of the female, and the female could control fertilization by controlling whether sperm entered the spermatheca. It further showed that female adults had the ultimate control over fertilization. These structures or tissues had evolved to adapt to the movement, mating and other behavioral activities of the aedeagus. This study will provide a theoretical basis for understanding the reproductive physiology, evolution and diversity of insects as well as the insect behavioral mechanisms of mating and aedeagus movement.