01 - Preheat oven to 350°F. Pat duck dry with paper towels and prick skin all over with a sharp knife or skewer, taking care not to pierce the meat.
02 - Season duck cavity and skin evenly with salt and black pepper. Stuff cavity with quartered orange, onion, and thyme sprigs.
03 - Place duck breast-side up on a rack in a roasting pan. Roast for 1 hour, draining excess fat from pan every 30 minutes.
04 - While roasting, combine orange juice, orange zest, honey, soy sauce, grated ginger, minced garlic, vinegar, and chili flakes (if using) in a small saucepan. Simmer over medium heat, stirring occasionally, until glaze thickens and becomes syrupy, about 10 to 12 minutes. Set aside.
05 - After 1 hour, brush duck all over with glaze. Return to oven and roast for an additional 30 to 40 minutes, glazing every 10 to 15 minutes, until skin is deep golden brown and crispy. Internal temperature should reach 165°F.
06 - Remove duck from oven, loosely cover with foil, and let rest for 15 minutes before carving. Serve with remaining glaze.