Preheat oven to 350°F (175°C) and line an 8x8-inch metal baking pan with overhanging parchment paper.
Mix crushed graham crackers, melted butter, and sugar. Press firmly into the bottom of the pan and bake for 8 minutes.
Prepare brownie batter. Pour exactly half the batter over the crust and bake for 15 minutes.
Melt caramels and heavy cream in a saucepan over low heat until smooth. Remove brownie pan from oven, scatter pecans over the baked layer, and pour the warm caramel over the top.
Gently spread the remaining raw brownie batter over the caramel layer to seal it in.
Bake for an additional 20-25 minutes until the top is set. Remove and immediately sprinkle with flaky sea salt.
Allow to cool completely at room temperature, then chill in the refrigerator for at least 2 hours before slicing with a hot, clean knife.