Her majesty has addressed hundreds of members at Church House in Westminster after attending a service at Westminster Abbey.
She said: "The last Synod will be particularly remembered for the way in which, after prolonged reflection and conversation, even in the midst of deep disagreements, it was able to approve the legislation to enable women to be consecrated as bishops.
"This new Synod too will have to grapple with the difficult issues confronting our church and our world.
"On some of these there will be many different views."
The General Synod will discuss climate change and the refugee crisis.
The issue of how the Church treats and ministers to gay people is not expected to be raised until the next meeting in July.
Most of the sexuality discussions will be held behind closed doors.
The Archbishop of Canterbury, Justin Welby, said the meeting came at a time of "great uncertainty and conflict in the world".
He told the Queen he would "draw strength from knowing your prayers are with us".
Delivering the sermon at the service preceding the Synod, Father Raniero Cantalamessa, a Catholic who is Preacher to the Papal Household, told Church of England bishops that sexuality should not have divided Christians.
Speaking before the congregation moved to Church House, Father Cantalamessa called for unity between the different denominations.
He said: "We should never have allowed issues like sexuality to divide us more than faith unites us.
"Nothing is more important than to seek Christ's heartfelt desire for unity."
He told a packed Westminster Abbey that "the majority live and die around us as if he (Jesus) had not existed".