Joined by the Duchess of Cambridge, they toured the White Garden in the grounds of Kensington Palace.
As rain fell, William, Kate and Harry sheltered under umbrellas as they walked around the garden, of which Diana was particularly fond.
Thousands of white flowers and foliage – inspired by memories of Diana’s life, style and image, such as her white “Elvis” Catherine Walker dress – have been planted around the existing Sunken Garden.
The West London palace was Diana’s home until she died on 31 August 1997 in a car crash in Paris.
It became a focus for thousands of mourners who came to leave flowers and remember her.
Fans of Diana have already begun leaving floral tributes and pictures of the princess at the gates of her former home to mark the two decades since she died.
The princes were due to meet past and present gardeners, as well as representatives from the charities supported by Diana in the final years of her life, including Great Ormond Street Hospital, the National Aids Trust, The Leprosy Mission, Royal Marsden Hospital, English National Ballet and Centrepoint.
Before the visit, a Kensington Palace spokeswoman said: “Together, they will reflect on the significant achievements of the Princess, and the legacy of her work which continues to resonate with so many today.”
Later this year, the princes plan to erect a permanent statue of their mother in the palace grounds “to recognise her positive impact in the UK and around the world”.
In interviews described as the most personal they have ever given about their mother, the princes have described the personal anguish they experienced and the “raw” grief they still feel.
They have spoken of their regret over a “desperate rush to say goodbye” during their final phone call with their mother on the night she died.
The pair have also released three of their favourite photos from an album put together by Diana, including one where she is holding Prince William at the time she was pregnant with Prince Harry.