The popular attraction, located near St Austell, beat both Foster and Partners' 'Gherkin', at 30 St Mary Axe, and the McLaren Technology Centre, also by Foster, in a poll by YouGov for Constructionskills, the skills council for the construction industry.
Eden Project chief executive Tim Smit said: 'Eden was built for the nation, so obviously we're tickled pink that it has found such a place in the heart of the Great British public.
'If there's one thing that all the shortlisted projects have in common it is that they are sexy, challenging and inspiring.'
The results revealed that almost half those in the Tyne Tees region favoured the Gateshead Millennium Bridge. In Scotland, 45 per cent of respondents said that the Scottish Parliament was their favourite Modern building and in Wales it was the Cardiff Millennium Stadium which came out top.
In order of preference, the buildings that are most popular nationwide are: the Eden Project; 30 St Mary Axe; McLaren Technology Centre; the Great Court at the British Museum; Gateshead Millennium Bridge; Cardiff Millennium Stadium; the Millennium Bridge in London; the Scottish Parliament; Selfridges in Birmingham and finally, Tate Modern.