Place a large bowl on a double boiler over medium heat and melt the butter and chocolate. Stir frequently with a silicone spatula and ensure the bottom of the bowl does not touch the water (this will avoid the chocolate scorching).
Remove the bowl from the heat and place it on a heat-safe surface. Be careful because the bottom of the bowl will likely be hot.
Whisk the sifted cocoa powder into the melted chocolate mixture until no clumps remain. Then, add the sugar and combine.
Whisk in the eggs and vanilla until the mixture becomes thick and glossy.
Add the pieces of cream cheese to the bowl and use a fork to mash it and incorporate it into the batter. Continue this process until only small pieces of cream cheese are visible.
Mix the salt into the flour in a separate bowl before pouring into the batter. This will ensure the salt is evenly distributed throughout the brownies. Pour the flour mixture into the batter and stir until almost fully combined.
Add pecans and fold into the batter until evenly incorporated and no flour streaks remain.
Pour batter into the prepared pan and smooth the surface using an offset spatula or the back of a spoon.