In a large bowl, mix together beef, grated onion, stuffing mix, soup, eggs, thyme and pepper until well combined. Form into a loaf and transfer into the loaf pan.
Bake for 45 minutes
Remove meatloaf and top with shredded cheese, Parmesan and crispy onions. Return to oven and bake 15 minutes more.
Remove to cooling rack, lift meatloaf from pan, transfer to a patter and rest 10 minutes before serving.