The A63 Castle Street Development Consent Order - the means of obtaining permission for developments categorised as Nationally Significant Infrastructure Projects - was submitted today.
The planning inspectorate will organise a number of hearings in Hull next year so bodies like the Ramblers will get a chance to make representations.
They have expressed concerns that taking all the crossings out on a half-a-mile stretch - apart from the new bridge and the Myton Bridge underpass - will leave people struggling to cross in future.
Highways England said the scheme - which aims to ease congestion on the road to the port - was still on track for construction work to start in 2020.
Senior project manager James Leeming said: “Subject to the outcome of the Development Consent Order examination by the Planning Inspectorate, and to the Transport Secretary’s decision regarding a development consent order application, the proposed scheme is on target for construction work to start in 2020.
“The upgrade is part of the government’s £15 billion roads investment strategy, which is transforming the road network and improving connections between cities."
Dr Ian Kelly, chief executive of Hull and Humber Chamber of Commerce said the "sooner it was done the better."
He added: "We are very pleased that it remains on time in terms of the current timetable. It is a positive step."