Objective To study how the anatomical morphological difference of pelvic floor system affects pelvic floor organ prolapse and explain the mechanism of pelvic floor organ prolapse. Methods A two-dimensional sagittal biomechanical finite element model of pelvic floor was developed based on MR Images of normal physiological pelvic floor and prolapsed pelvic floor. The relationship between the overall shape and position characteristics of pelvic floor and pelvic floor organ prolapse was compared under the action of abdominal pressure. Results Compared with the physiological pelvic floor, the maximum displacement increases percentage of cervix and anterior vaginal wall and genital hiatus are 152.7%, 695.2% and 476%, and the maximum displacement increase percentage of pathological pelvic floor is 513.5%, 1833.3% and 1572%, respectively. Cystocele, prolapse of anterior vaginal wall and uterus occurred in both cases, but no prolapse of pelvic floor organs occurred in physiological pelvic floor. Conclusions Changes in the initial morphologic characteristics of the pelvic floor organs will lead to alterations in the pelvic floor's supportive function and stress areas, ultimately making it more susceptible to organ prolapse under abdominal pressure. Furthermore, the change in the initial morphologic characteristics makes the pathological pelvic floor lack the corresponding support function, which is more likely to make the pelvic organs and tissues under the influence of other factors to undergo a greater change in the morphologic characteristics and may lead to other organs and tissues in the pelvic cavity fascial injury, thereby leading to a more serious prolapse phenomenon.