Upgrades to each of the Eye's 32 capsules will allow for more energy-efficient heating and ventilation.
Electricity costs will be cut through improved airflow through the capsules, keeping them cool in summer.
Individual capsules will be repaired one at a time.
They will be removed from the wheel and ferried down the River Thames to Silvertown, at the heart of London's docklands.
David Sharpe of Merlin said: "This work will ensure the London Eye operates at maximum efficiency and is cutting down its carbon footprint well into the future."
The London Eye is one of the most popular attractions in the capital and receives around 10,000 visitors a day.
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