Every tearoom that Sugimoto creates is formally named, and the one in this apartment is called “Ukitsubo,” which means “floating inner garden,” a reference to the 11th-century novel “The Tale of Genji,” which is set within the wealthy, refined Heian court. One of Sugimoto’s original ideas was to create an indoor garden. But that was impossible in a tower, and so instead, he chose to place the two bonsai trees in a rectangular garden in the dining room, a 10½-foot-long slab of Komatsu stone between them. If the windows offer a lightness, a moment to pause in time and drift into infinity, then the two bonsai, whose dense, visible surface roots (nebari, which are considered a balance to the tree’s sinuous branches) return you to earth.

Sugimoto also insisted on using as many premodern materials and techniques as possible. The lustrous smoky black square tiles that blanket the hallway are clay, handmade by a ceramist in Nara, near Kyoto, whose ancestors made the tiles for the centuries-old Todaiji temple. They are intended to be used on roofs, but Sugimoto prefers them for the floor because of the particular way they reflect the light. The walls are covered in soft-white Japanese shikkui plaster, which was carefully applied by trained craftsmen — though it is smooth to the touch, their strokes glint unevenly in the natural light. The kitchen cabinets are entirely covered in long metal sheets hammered by hand. Nearly all the apartment floors are clad in splendid planks of unfinished cedar (the notable exception is the master bedroom, whose floors are laid with chestnut, the wood hand-scooped to lend it a dappled effect; Sugimoto calls the sensation of walking on it “a free foot massage”).

SUGIMOTO IS NOT a licensed architect, though he doesn’t really care for labels. As he wrote in the chapbook he created about the apartment for his personal collection: “Recently, architecture is getting closer to art while art is becoming more architectural; seldom, however, does one hear of them coming together in a beautiful or harmonious manner. Architecture’s sense of inferiority to art and art’s own jealousy of architecture are inextricably entangled.” His first foray into architectural work was restoring the medieval Go’o Shinto Shrine on the island of Naoshima, in 1996. He subsequently opened an architecture practice in Japan under the name New Material Research Laboratory with Tomoyuki Sakakida, a trained architect. New Material has completed a number of noteworthy buildings, including the Enoura Observatory, which is part of the Odawara Art Foundation that Sugimoto founded in 2009 on the coastline of the Kanagawa Prefecture, just south of Tokyo. Enoura’s cantilevered main gallery with glass walls is elegantly oriented to glimpse the sun as it rises from the east. The firm’s name, however, is cheekily disingenuous; Sugimoto is fond of repurposing ancient materials. In the Manhattan apartment, the dining room floors are planks of Yakusugi — cedar from Yakushima island that is more than a thousand years old. (It is now illegal to harvest the forests of Yakushima; the wood he used had been in storage for some time.) For centuries, the wind ripped across the island, causing the growth rings of the trees to bend and swirl into mesmerizing shapes. Several of the stones placed around the house — one as a decorative end piece to a hallway, another as a step to the tearoom — are from centuries-old Japanese gardens, now vanished. Sugimoto has long admired the patina of unfinished cedar in Nara’s temples, where the wood’s color has transformed over time from tawny yellow to a mossy gray. “After 1,200 years, beautiful,” he remarked. “It gets darkened. The surface is still beautiful.” He pauses. “But whether this building survives 100 years ...” He didn’t need to finish that thought. We both knew none of us would be here to find out.