The space in Queen Elizabeth Olympic Park will feature 33 blossoming trees, to represent the different boroughs.
The species of trees have been chosen in particular because this year's blossom season coincided with the start of the first lockdown.
London's mayor said it would be a space where people could "reflect".
The Queen Elizabeth Olympic Park, in Stratford, was originally built for the 2012 London Olympics and has been further developed into a public space since.
The trees will be planted in three rings in the north of the park early next year.
Sadiq Khan said it would be "a permanent reminder of the lives that have been lost, a tribute to every single key worker, and a symbol of how Londoners have stood together to help one another".
City Hall is working with the National Trust and Bloomberg to create the "lasting living memorial".