The Most Rev Justin Welby said on social media on Wednesday it was "easy to tell MPs how badly they are doing, easy to abuse and threaten".
But the archbishop said MPs "deserve respect" and urged people to pray for them and for a "decision that has widespread support".
He said: "It's easy to tell MPs how badly they are doing, easy to abuse and threaten. But they have to decide for us and deserve respect.
"Let us pray for them (or intend well if not pray), for a decision that has widespread support and for a process that brings national agreement."
In a further tweet, Mr Welby added: "Reconciliation is less about agreeing than about finding out how to disagree well.
"We must respect the vote of the people and unite our country #hopefilledfuture."
His comments come on the same day MPs will vote on which kind of Brexit they favour.
The archbishop has previously called for reconciliation over Brexit, telling a House of Lords debate on leaving the EU "there is a requirement for national reconciliation".
Mr Welby told the Lords if both sides could not compromise then the country will face a no-deal Brexit.
He added: "There has to be an agreement in which all accept the need to deliver 'the will of the people', which was expressed in the referendum, while also recognising that when it was expressed in such a close result there is a duty to build in compromise - an inevitability, albeit unwelcome to some.
"If not there will be, by default, a no-deal Brexit. That outcome would be not only a political and practical failure but a moral one equally as serious as ignoring the result of the referendum entirely."
Mr Welby has also urged Remainers and Brexiteers to get together this weekend.
The Church of England is aiming to get people who disagree over membership of the bloc to "chat over a cup of tea and pray for our country and our future".
It also tweeted on Wednesday that its "Lent Pilgrim reflection" for today was around extreme forgiveness and quoted Luke 23.32-43: "Father, forgive them; for they do not know what they are doing."
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.
Tell us what you think about our news service, what you want and how Premier fits into your news landscape. Take our quick survey!