With the exception of the wooden wings and tails of the original M20 and M20A, M20s are all-metal, low-wing aircraft. The wings are of cantilever construction, consisting of a main spar and an auxiliary spar that extends from the fuselage to the mid position of the flaps. The wing skin is aluminum which is flush riveted in many areas to reduce parasitic drag. Slotted flaps cover 70% of the trailing edge. Early models use a hydraulic hand pump to control the flaps while later models have electrically operated flaps. The forward fuselage has a steel tube cabin structure covered in aluminum skin, while the aft fuselage is of semi-monocoque design.

The tricycle undercarriage legs of the Mooney M20 models are made of heat-treated chrome-molybdenum steel. The main gear legs are attached to the main wing spar, while the nose gear is mounted onto the steel cabin frame. Rubber discs, as well as spring steel, around the legs allow for compression and shock absorption on landing. Except for the fixed-gear M20D, the nose wheel retracts rearward and the main wheels towards the fuselage. Early models use a hand-operated lever system to raise and lower the gear. Later models use an electrically operated landing gear retraction system with a backup crank-operated or wire-pull gear extender.

The empennage of the Mooney M20 is easily recognizable by its unique tailplane with a vertical leading edge. (The tail looks like it is "leaning forward", but it is actually straight vertical.) The horizontal tailplane, which consists of a fixed stabilizer and trailing elevator, has no trim tabs. The entire tail assembly pivots at the rear of the fuselage to provide for pitch trim.

All M20s store fuel in two separate "wet wing" tanks, which are located in the inboard sections of each wing. Fuel is driven from the tank to the injectors or carburetor by an engine-driven pump, backed up with an electric boost pump.

For increased power many M20s also have a ram air system called the Mooney "Power Boost". For normal operations the intake air is filtered before it enters the induction system. When ram air is selected, partially unfiltered air will enter the induction system with a higher pressure and consequently the manifold pressure will increase about a full inch when flying at 7500 msl, giving a greater power output.  The turbocharged variants omit this feature as they have their own "power boost" that provides far more increase in manifold pressure.