Reimagining Europe is a joint project between the Church of England and the Church of Scotland.
Archbishop Justin said there would "be passionate arguments on both sides" as the UK approached the referendum, which has been promised before the end of 2017.
"People will say that we should not take the risk of leaving, others that it is less of a risk than staying," he said.
"There will be talk of national sovereignty, of national confidence, of repatriation of laws, or being bound by European laws over which we have no control. The only certainty is that there will be much heat, probably slightly less light, but that it is a hugely important decision, with thoughtful and committed people, including Christians, on both sides."
He added: "This new blog is a contribution to the debate. It is a joint initiative between the Church of England and the Church of Scotland, whose mediating and reconciling role during and after the Scottish referendum campaign is something we should all look to as a model for how the Church can engage in divisive debates.
"It is a platform on which we can seek out new ways of disagreeing well that leaves us energised and revitalised, not dispirited and divided."
The Revd Dr Angus Morrison, Moderator of the General Assembly of the Church of Scotland, said: "This blog is a platform for various voices to share their ideas, but most importantly for readers to learn and reflect.
"It will have contributions from a range of perspectives. Its purpose is not to campaign, but that all of us may gain in understanding and respect for political ideas even, or particularly, if we find ourselves in disagreement.
"Unlike the Scottish independence referendum, where the Church of Scotland chose to remain impartial, our General Assembly does have a longstanding view that continued EU membership is in the best interests of Scotland, Britain and the EU."