Cook 1 lb. medium tube-shaped pasta (such as rigatoni, penne, or calamarata) in a large pot of boiling salted water, stirring occasionally, until al dente. Drain, reserving 2 cups pasta cooking liquid.
Meanwhile, heat ¼ cup extra-virgin olive oil in a large Dutch oven or other heavy pot over medium. Cook 1 medium white onion, finely chopped, 6 garlic cloves, finely chopped, and 1½ tsp. crushed red pepper flakes, stirring often, until onion is softened, 10–12 minutes. Add one 15-oz. can unsweetened pumpkin purée and cook, stirring often, until warmed through, about 5 minutes. Stir in ½ cup heavy cream and 1½ cups pasta cooking liquid.
Add pasta to sauce and cook, tossing and adding more pasta cooking liquid ¼ cup at a time if needed, until sauce coats pasta, about 2 minutes. Add zest of 1 large lemon and 2 oz. Parmesan, finely grated (about 1 cup); toss to combine.
Divide pasta among shallow bowls. Top with more Parmesan and red pepper flakes.
