The Trust tried to get the development stopped because it is so close to the UNESCO world heritage site but failed in a judicial review.
The Northern Ireland Executive's Environment Minster Alex Attwood had originally given planning permission for the development in February 2012 and Mr Justice Weatherup has now rejected all grounds of challenge of that original decision.
Work on the 365-acre site, to be known as Bushmills Dunes Golf Resort and Spa, will now start as soon as possible.
The site will see the building of an 18-hole golf course, a five-star 120-bedroom hotel and 70 golf lodges which could lead to up to 360 new jobs.
The National Trust said they were not only unhappy with the decision but feared that it could lead to similar developments elsewhere.
"We still believe that if a development of this scale does go ahead in this location, the message is that nowhere in Northern Ireland, no matter how important or protected, is safe from development," they said in a statement.
"The ruling today has served to highlight aspects of very serious concern for those partners involved in the care and protection of the world heritage site."
In his ruling Justice Weatherup said that his court was not obliged to follow UNESCO's convention when dealing with new developments.
"The court must step away from seeking to implement, directly or indirectly, what obligations there may or may not be under the convention," he said.
"I must not grant to citizens of the state a right that only exists in international law, if it exists at all."
However, he did not order the National Trust to pays cost over the appeal by conceding that there were "a multitude of reasons why the National Trust was warranted in bringing this application."
North Antrim MP Ian Paisley Jr. on the other hand was furious the National Trust were even allowed to go ahead with the judicial review.
"Their actions I still believe have been disgraceful and damaging for the Northern Ireland economy, but we must take heart in today's decision and look to move forward as the course progresses," he said.
Golfer Darren Clarke described those appealing the plan as "treehuggers" and pointed out that the development was further away from the Causeway than the National Trust's own hotel and car park.
US-based Northern Irishman Dr Alistair Hanna, who is heading the project, said the development will be one of the "most spectacular golf developments ever seen in Ireland".
"Not only will the resort provide a world-class golf links course and facilities attracting thousands of visitors each year, it will also protect the vulnerable topography of the coastal area which has been left vulnerable following decades of neglect," he said.
Co. Antrim's Giant Causeway is an area of about 40,000 interlocking basalt columns, the result of an volcanic eruption estimated to have occurred over 50 million years ago.