The Duke of Edinburgh, the Duke and Duchess of Cambridge, Prince Harry and a host of dignitaries will also be at the church.
In her message to mark the day the Queen will urge people to "support those in need" and others who "feel excluded".
"Today, and in the year ahead, the theme An Inclusive Commonwealth is an inspiration for us all," she said.
"Let us give it practical effect by supporting those in need and those who feel excluded in all walks of life. By doing so, we will continue to build a truly representative Commonwealth community."
The Commonwealth has 53 member countries representing 2.3 billion people, of which 60% are under 30.
Her Majesty also said working together for the common good was an essential ingredient of belonging to the family of nations.
The monarch wrote: "Each of us has cause to celebrate the sense of belonging expressed in our 2016 theme: An Inclusive Commonwealth.
"Our recognition of this value, and the wisdom of mutual respect for each other, is set out in the Commonwealth Charter. Its opening words, 'We the people of the Commonwealth' convey the conviction that individuals, as well as governments, build and shape our success.
"Being inclusive and accepting diversity goes far deeper than accepting differences at face value and being tolerant.
"True celebration of the dignity of each person, and the value of their uniqueness and contribution, involves reaching out, recognising and embracing their individual identity."
The service will be the largest annual inter-faith gathering in the UK.
Highlights will include the principal reflection given by Kofi Annan, former secretary general of the United Nations, and a musical performance by Ellie Goulding.