Step 1

Preheat oven to 275 degrees F (135 degrees C).

Step 2

Rub beef roast with sea salt and black pepper. Heat a large cast-iron skillet over medium-high heat; sear roast on all sides in the hot skillet, 2 to 3 minutes per side. Turn roast so the ribs and fat side are facing up.

Step 3

Roast prime rib in the preheated oven for 45 minutes; scatter onion quarters around roast and continue cooking until an instant-read meat thermometer inserted into the thickest part of the meat reads 130 degrees F (54 degrees C) for rare, about 2 more hours.

Step 4

Remove roast from skillet, wrap meat in aluminum foil, and let rest for 15 to 20 minutes to let juices reabsorb into the meat. Leave onion pieces in skillet.

Step 5

Pour drippings from skillet into a bowl and skim off excess grease. Return degreased drippings to skillet with onion pieces, place over medium heat, and melt butter in the drippings. Whisk flour into mixture to make a paste, 1 to 2 minutes. Stir red wine into flour paste until smooth. Mix beef stock into pan gravy until smooth; stir thyme sprigs into gravy.

Step 6

Reduce heat to low and simmer gravy until thickened, 5 to 8 minutes. Strain gravy, discard onion pieces and thyme, and serve with prime rib.