Preheat oven to 350 degrees F (175 degrees C). Place flounder fillets in a 9x13-inch baking dish.
Mix lime juice, parsley, and salt together in a small bowl. Pour over fillets.
Melt butter in a large skillet over medium heat. Add olive oil, onion, red bell pepper, orange bell pepper, jalapeno pepper, and garlic; cook and stir until tender, about 8 minutes. Stir in tomatoes, orange juice, jerk seasoning, salt, and pepper; bring to a boil. Remove from heat.
Spread 3/4 of the onion mixture over the fillets in the baking dish.
Bake in the preheated oven until fillets flake easily with a fork, 10 to 13 minutes. Let stand for 5 minutes before serving. Serve remaining onion mixture alongside fillets.