St. Mary's Cathedral's structure is impressive.it has 8 curved walls which are almost perpendicular and form a large cross in an aerial view. The brightness of the stainless supports on the outside symbolizes the light that Christ makes shine upon the world and in the heart of men. The hard walls of pre-cast concrete evoke the words of the Bible: "The Lord is my rock and my salvation, my deliver is my God" (Psalm 18:3). They show how God is the pillar and the foundation of all men. "Come to me, all you who labour and are overburdened, and I will give you rest" (Mt. 11:28).

The bell tower outside has four sides that appear flat at first glance but in fact hyperbolic, and stretch up into the sky in a single line. The four bells were imported from Germany. The designer, through studies of different bells in Japan, has made a real effort to bring out a sound adapted to the Japanese sentiments.

The pipe organ is the largest pipe organ in a Japanese church. It is made in Italy by Mascioni Organs and installed in 2004. It was especially designed to match the cathedral interior. It has 3 manual keyboards with 58 keys.

The Grotto of Lourdes resembles closely the one in Lourdes. It was built by the French missionaries to show their faith to the Blessed Mother.