Most Revd Justin Welby used his presidential address to tell members he had two main fears for the Synod.
"If I might begin with the worst," he said, "one of my fears is that we approach this Synod as a place of suspicion and conflict."
He added: "To use Pope Francis' phrase, we cannot come together in a 'hermeneutic of conspiracy'.
"Many of you will remember the performance of Kenneth Williams in 'carry on cleo', in which as he faces his murderes, he cries out 'infamy, infamy, they've all got it in for me'."
The archbishop said the system of Synod suggested one side must win and the other lose.
This was not the case, he said: "If any lose, we all lose. If any win, we all win".
But he said the Church must not be ashamed that it has its "arguments in public".
"It is healthy and good," he said.
He told members there was still an interest in what the Church does despite those who "assert the lack of relevance of the Church of England".
Archbishop Justin cited the Church's discussions on sexuality as a successful way Christians were able to discuss a controversial issue in a respectful way but he accepted the next five years of Synod offered 'enormous challenges to the future of the Church'.
The events in Paris, in which 130 people died in an Islamic State terror attack, meant the Church could not turn in on itself: "We will not likely ever be forgiven if this Synod turns inwards," Archbishop Justin said.
The attacks did not mean a "war against Islam" he stressed, adding that Christianity too had extremists.
"The task is to overwhelm extremism not by other extremes but with hope and love," he said.
The Archbishop ended his address by telling members he hoped they could look back in five years time as "people who have built together, who have listened and heard, and although not agreed, have done our best to be faithful to Jesus Christ".