Horizon Nuclear Power submitted 41,000 pages to support its development consent order application last month.
Following the statutory 28-day period of review by the Planning Inspectorate to ensure it met the standards required, it has now been accepted.
Also, four other key environmental permits have been cleared to begin their assessment by Natural Resources Wales.
Duncan Hawthorne, CEO of Horizon Nuclear Power, said: “This is a significant milestone for Horizon and an important step on the path to having all the permissions we need to build Wylfa Newydd.”
The approvals come after energy secretary Greg Clark confirmed that Wylfa Newydd is the next project in the UK’s nuclear new build programme.
He also confirmed formal negotiations between Horizon and the UK Government were underway on financing support for the £14bn project.
The Inspectorate has three months to make recommendations to the Secretary of State who then has a further three months to make the decision on whether to grant or refuse development consent.