The large delta wing of the SR-71 did not lend itself to have separate elevator and aileron control surfaces but instead utilized elevons, a single control surface that combines elevator and aileron inputs. Mechanical pitch and roll inputs from the control stick were blended in a mixer assembly, located in the tail of the aircraft, to actuate the elevons and move the aircraft accordingly.

The two large rudders were fully moveable surfaces, unlike conventional aircraft having a vertical stabilizer with a trailing rudder control. Each rudder assembly was canted inward 15 degrees for increased directional control and to reduce radar returns off the aircraft. At cruise Mach, having the rudders streamlined was important for good imagery results as well as for aircraft performance. To center the rudders, the pilot had to visually align each rudder separately using the periscope.