Mills scored 102 goals for Whitehawk after joining the club in 2012, having previously had spells with clubs including Peterborough and Torquay.
Details of the length of the 26-year-old's contract at Stonebridge Road have not been disclosed.
Mills is Ebbsfleet's first signing since winning promotion from National League South in May.

The monitoring of paramilitary activity in Northern Ireland was conducted by the IMC up until 2011.
The PSNI has previously said it would support any move to set up such a body.
Lord Alderdice, who is also a former leader of the Alliance Party, said he did not think it would be appropriate for the commission to return now.
Talks will begin next week in Belfast in a bid to resolve the current crisis,  sparked by the murder of ex-IRA man Kevin McGuigan Sr.
Police believe that killing was in retaliation for the murder of former IRA commander Gerard Jock Davison in the Markets area of Belfast in May.
The Ulster Unionists withdrew from the executive after police said Provisional IRA members had a role in the killing.
"The current crisis is of a different order," Lord Alderdice told BBC Radio Ulster's Talkback programme.
"Even before the horrible murders of these two men, we were right on the edge of devolution being set aside.
"If somehow or another, magically, the issue of these two murders was taken out of the picture, we would still be in that position of crisis where the assembly, the executive, is about to be suspended or fold because there is no agreement on the governance of Northern Ireland.
"The IMC or any new IMC could not help that problem at all, it did not have a political mandate to try to get people to negotiate on the politics and the governance issue.
"I think it is maybe unwise for people to look back at a form of treatment that worked before and say: 'Oh well the symptoms are the same so the diagnosis is the same'."

The IMF said the mainland should reduce foreign exchange intervention.
China's currency is widely seen as undervalued and the country was accused for years of suppressing the yuan in order to boost exports.
China says it is trying to manage the yuan's value against other currencies.
Analysts say that in reality it is still pegged to the dollar.
The IMF also said fiscal stimulus should be China's "first line of defence" in its economic slowdown.
It predicted China's growth would stabilise at around 6% by 2017.
The IMF also recommended there should be an emphasis on supporting private consumption.
China's economy grew by 7% in the first quarter of the year, a large figure by Western standards, but the lowest for the country since the financial crisis of 2009.
Last year its growth slowed to its weakest in 24 years, expanding by 7.4% in 2014 down from 7.7% in 2013.
Foreign exchange and reform
In April, the US Treasury Department said China's currency needed to appreciate further "to bring about the necessary internal rebalancing towards household consumption".
It did not label the country as a currency manipulator, however, and said China had made progress, with its "real effective exchange rate appreciating meaningfully over the past six months".
But the US said further appreciation was needed to prevent the yuan becoming more undervalued, particularly as the mainland continued to see productivity growth greater than its major trading partners.
In its latest economic outlook for the Asia Pacific the IMF said the mainland needed reforms that "reorient the economy away from excessive reliance on real estate, heavy industry, and external demand".
It said China should implement "without delay" a blueprint of reforms that was introduced in 2013 - including a clampdown on risky credit activity such as shadow banking.
It said the reforms were critical to sustainable growth.
In its Thursday report, the IMF forecast an expansion of 5.5% for the wider Asia Pacific region over the next two years.
Consumption was the main engine of growth across the region, it said, except in Japan where consumption was not as robust.
It said world growth would to pick up modestly to 3.5% in 2015 and to 3.7% in 2016.
Newly-promoted National League side Ebbsfleet United have signed former Whitehawk striker Danny Mills.
[NEXT_CONCEPT]
The ex-chair of the Independent Monitoring Commission (IMC) has said he does not believe bringing it back would solve the latest Stormont crisis.
[NEXT_CONCEPT]
The International Monetary Fund (IMF) has said China should continue to provide "greater flexibility" in its exchange rate policy as the country continues to see slower growth.