The award, for her "outstanding contribution" to global conservation was accepted on her behalf by the Duke of Sussex at a ceremony in Sydney.
The tribute, from the Australian Geographic Society, recognises the impact of the Queen's Commonwealth Canopy, an initiative launched in 2015.
Chrissie Goldrick, editor-in-chief of Australian Geographic, said the Queen had offered "vital leadership" to a project that "aims to tackle deforestation on a global scale".
After its launch, she said: "So far 42 countries of the 53 that comprise the modern Commonwealth have added over 90 projects to the canopy in a very short time. It is an idea that has really taken off."
Ms Goldrick described Harry as "a passionately committed conservationist" and said that while in Australia he had made "the most of your popularity, your influence and your undoubted charisma to draw attention to a range of issues close to your own heart".
She added: "When people like Your Royal Highnesses, held in such affection by so many, when you speak, people listen - you can change hearts and minds."
Prince Harry added the K'gari/Fraser forest to the Queen's Commonwealth Canopy during a visit to Fraser Island on Monday.
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