In large nonstick saucepan over medium heat, melt butter. Add celery, onion, carrot, pepper, and thyme. Sauté until vegetables are tender, 10 minutes.
Stir in flour until well blended. Stir in broth. Increase heat to medium-high. Add broccoli, cauliflower, and pearl onions. Bring to boil, then lower heat and simmer, uncovered, 15 minutes. Remove saucepan from heat. (If making filling ahead, let cool to room temperature. Cover and refrigerate.)
Preheat oven to 400°F. Spread vegetable mixture in 9-inch glass or ceramic pie plate. Top with cheese. Cover filling with pastry. Trim edges. (If crust is not lattice, cut 6 long slits in it to vent steam.) Place dish on baking sheet.
Bake until pastry is golden and filling is bubbly, 25 to 30 minutes. Let stand 10 minutes