The structure of your game design document is completely up to you, but one I create tends to include (note that this works better for RPGs or other story-driven games):
Table of Contents - Very important, as once you have more complex games you will need to include an organization method
Description of the Game - A brief description of the game, giving some descriptions of game-play, along with platform and other important details
Story overview - Give an overview of your plot
Controls - List the controls you will be using in your game
Tech requirements - You can go into more detail about platform here
Game Flowchart - Show how your game's screens connect
Presentation - Give details about camera type, HUD, and other info the player will see
Player Character - Give information about your player, such as what they look like, backstory, and tools/weapons they may use
Combat - Describe how combat works (if applicable)
Game Levels - Give some examples of levels
Enemies - Give details about your enemies (attacks, looks)
Bosses - Information about specific bosses
NPCs - Describe AIs that don't attack your character
Music/SFX - What music and SFX need to be produced
Appendices - Place long lists here along with scripts and any other information
You may also want to create a more concise version of your game design document which is about one page, containing the following things:
Title and Concept Overview - Give a brief overview of what the game is like and what players will do
Platform - List the platform the game will be published on
Main Points - Give the very basic info about your game, such as it being an FPS, an MMO, and having a single-player mode
Summary - Summarize your plot, if any
Characters - Give some info about your characters