Congenital megalourethra is a rare prenatal finding while prenatal diagnosis of imperforate anus poses high challenge. This is the first prenatally ultrasound diagnosed case which had congenital megalourethra and imperforate anus. This case demonstrated the possibility of using the prenatal imaging findings to evaluate the postnatal prognostic outcomes in multi-organ anomalies. We present a case of congenital megalourethra, diagnosed prenatally at 22 weeks' gestation, in which the penis appeared severe dilated with complete absence of the corpora spongiosa and cavernosa. This case also revealed absence of perianal muscle which was in associated with imperforate anus. Detailed prenatal ultrasonographic findings predicted the high possibility of poor outcome of the fetus in the pulmonary, renal, and sexual functions. This case serves to identify not only the marked bilateral hydronephrosis features but also the striking lower urethral malformation with obstruction flow effect of the penis. Indeed we believe this is the first case report of a rare case of fetal megalourethra associated with imperforate anus at early second trimester on ultrasonography imaging.