The online service was launched alongside Metal Gear Solid 4: Guns Of The Patriots and has been supported with numerous expansion packs and updates since its release.
The closure will begin with the removal of the Metal Gear Online shop and character creation tools in April.
For the time being, expansion packs SCENE, GENE and MEME will be available to download for free, giving players access to additional characters and new gameplay stages.
More than one million members signed up to the service within the first six months of its release.
The news comes days after analysts predicted a 2013 launch for Metal Gear Solid 5.
> Read our Metal Gear Solid HD Collection review
Watch the launch trailer for Metal Gear Solid HD Collection below: