Preheat oven to 325°F (163°C). Grease a springform pan with butter or non-stick spray and place it on a rimmed baking sheet to catch spills.
In a large bowl, whisk melted butter, granulated sugar, cocoa powder, and sea salt until smooth. Stir in vanilla extract.
Add eggs one at a time, mixing well after each addition. Fold in flour until just combined.
Spread brownie batter evenly into the prepared pan. Bake about 15 minutes, then cool completely.
Beat cream cheese in a large bowl until smooth. Add both sugars and heavy cream; beat until creamy.
Add eggs one at a time, mixing just until combined. Stir in vanilla extract.
Pour cheesecake mixture over cooled brownie base. Tap pan gently to remove air bubbles.
Bake for 55 to 60 minutes until the cheesecake is mostly set. Turn off oven, crack door open, and let cool inside for 10 minutes.
Remove from oven, cool completely on a wire rack, then refrigerate at least 4 hours or overnight.
Release cheesecake from pan and transfer to a serving plate. Drizzle caramel sauce over top and sprinkle with flaky sea salt if desired.
Slice with a knife warmed under hot water and serve chilled or slightly above refrigerator temperature.