THE HARD WAY:
When Draygon swoops down at you, aim for its belly, and shoot Super Missiles/Missiles. If you run out of Missiles, switch to Charged Beam shots. The difficult part is dodging its sticky blobs that it spits at you, which allow it to pick you up and spank you with its huge tail.
THE EASY WAY:
Allow Dragon's sticky blobs to touch you and let Draygon grapple on you and spank you with its tail. While you are in the air, equip the Grapple Beam. When you are at the correct height in front of the broken cannons on the wall that shoots sparks (you can destroy them with a Super Missile), shoot the Grapple Beam straight ahead. The surge of electricity conducts through Samus and onto Draygon, killing it in a matter of seconds.