Objective To analyze the diagnostic value of transperineal sonography and magnetic resonance imaging (MRI) in female pelvic floor dysfunction (PFD). Methods The clinical data, transperineal sonography and MRI data of 84 patients with pelvic organ prolapse (POP) (observation group) and 84 healthy women (control group) at the same time were analyzed retrospectively. The results were compared, and the detection conditions and diagnostic value of the two examination methods were analyzed. Results MRI examination showed that the decreasing distances of bladder neck, cervix and anorectum when breath holding (Valsalva movement) were all significantly higher in the observation group than those in the control group (P<0.05). Transperineal sonography showed that the distances from the lowest point of bladder neck, cervix and rectal ampulla to the inferior margin of pubic symphysis in the observation group were lower than those in the control group (P<0.05). A total of 128 lesions of prolapses were detected in 84 PFD patients, of which 112 cases were detected by MRI and 94 cases were detected by transperineal sonography. There was no significant difference in specificity and positive predictive value between MRI and transperineal sonography diagnosis (P>0.05). The diagnostic sensitivity, negative predictive value and accuracy of MRI were higher than those of transperineal sonography (P<0.05). Conclusion Transperineal sonography and MRI are favorable for the diagnosis of POP, and the accuracy of MRI is higher than transperineal sonography.