The church is constructed in brick, and faced with local grey-green ashlar stone; it has slate roofs. The "external stonework was intended to be left 'untooled' ", because the architect "wished the church to appear as if it had sprung out of the soil, instead of being planted down on it". Its plan consists of a nave with north and south porches, and a chancel with north and south transepts. In the west end are two tiers of ogee-headed windows. Between the windows in the upper tier is a cross in relief. There are similar windows, asymmetrically placed, on the north and south sides of the church. On the roof, in a position to the west of the transepts, is a two-tier bellcote. In its lower tier is a round-headed arch containing the bell, with a smaller round-arched opening above. At the east end is a stepped buttress containing a round-arched lancet window, on each side of which is an ogee-headed window.
Interior
The interior of the church is rendered and painted, with "rich warm red" nave walls, a blue nave roof and "warm cream, almost a yellow" colour for the chancel. The nave has three-bay roof; its ceiling is canted and has a plain cornice. The north and south doors are in Art Nouveau style. These are constructed in oak and teak in chevron designs, and have mother-of-pearl decoration at the points of the chevrons. The lead font has a circular bowl carried on an octagonal column. It was cast at the Central School of Art and Design in London, and is decorated with leaf patterns and Christian monograms. The pulpit and retable were designed by Wilson, and are constructed from beaten and moulded copper. They are in Arts and Crafts style, the pulpit being decorated with grapes and texts from the Vulgate. The chancel is groin vaulted. The north transept contains an organ and in the south transept is a gallery. The stalls in the chancel are made from Spanish chestnut; they were designed by Wilson and carved by Arthur Grove with zoomorphic images. These include a hare, a tortoise, squirrels, rabbits, an owl, a mouse, a kingfisher, and a dolphin. The altar rails contain panels between large posts. The altar frontal was designed by Wilson; it is in cast copper and contains figurative panels. These depict, on the left, the Annunciation with the Virgin Mary and a dove facing a kneeling angel and, on the extreme right, the Rev Tooth and his guardian angel. The reredos is also in beaten copper; it depicts a vine springing from a chalice, and at the sides are bluebells springing from the monogram "IHS". The single-manual organ was built by Peter Conacher of Huddersfield in 1901.
The church is listed Grade I by Cadw because it is "a highly important and unaltered example of the work of Henry Wilson, a leading figure of the Arts and Crafts Movement. St Mary's , Brithdir ranks amongst his major works in Britain". It is "an exceptionally important and advanced work for its date". The church is considered to be "one of the few full blooded Arts and Crafts churches in Wales", and "one of the pre-eminent churches of the Arts and Crafts Movement". "The interior decoration and fittings are arguably the most complete and high-quality Arts and Crafts work in Wales."
