The initiative will support the charities Fare Share, which helps those facing food poverty and Home-Start which works with parents who need support.
The campaign will be launched throughout November with the aim to raise £5m for the charities.
The John Lewis Partnership recently stated its ambition to be a completely “different kind of business”.
Pippa Wicks, executive director of John Lewis and Partners, said: “In a year like no other, the world has changed – so we will be delivering a Christmas campaign like no other.
“During 2020 we’ve seen some inspiring and heartwarming acts of kindness throughout our country and our communities.”
Customers will be “encouraged” to support the campaign in five different ways including charity donations which the retailers said they would match by a value of £2m.
Some of the ways to support involve buying a variety of “exclusive and limited” edition campaign products, shopping in one of the two retailers’ and using the loyalty cards which will trigger an automatic donation to the two charities.
A further fund of over £1m has reportedly been created to ensure all of the retailers’ shops will be “actively partnering” with Fare Share and Home-Start and a range of local disadvantaged family charities in the communities they serve.
James Bailey, executive director of Waitrose and Partners, said: “This year has created even greater inequality in society with a catastrophic effect on some of the most vulnerable, and we are determined to play our part in addressing this.
“Everyone has a right to nourishment and a safe, warm home and we believe that as a Partnership, we can be an enduring force for good, which lasts well beyond Christmas.”
He added: “We don’t just want to talk about it, we want every customer, community and Partner to show their kindness in supporting these causes.”