Philip Hammond said demand from the Royal Navy was "just enough" to sustain one complex warship yard for the entire UK.
Outside the Union, the Scottish Government could never place enough orders to maintain the BAE yards on the Clyde, he warned.
In a speech to the Scottish Conservative Party conference in Edinburgh, Hammond sought to dismantle the SNP's post-independence defence policy, saying it rested on "fundamentally flawed" arguments.
He also warned independence posed a risk to some of the 12,600 defence industry jobs in Scotland.
He said the scale of the UK's defence capability, with a £34 billion annual budget and a £160bn 10-year equipment programme, meant the Union kept Scotland safer and more secure than it would be otherwise.
"Our greater scale delivers greater security," he said. "A separate Scotland could not hope to develop the same level of protection and resilience."
The SNP say that after a Yes vote, Scotland would get rid of Trident and establish a 15,000-strong defence force, with an annual defence budget of around £2.5bn.
It argues the Clyde yards would continue to win defence orders from the rest of the UK, even though the UK has never ordered a complex warship from a foreign state.
Hammond said: "The construction of the Royal Navy's new aircraft carriers alone, taking place just across the Forth Bridge, has already delivered hundreds of millions of pounds worth of work for the Clyde and Rosyth, with thousands of jobs in the shipyards linked to the programme.
"The overall drumbeat of shipbuilding work for the Royal Navy is just enough to sustain one complex warship-building yard - for the whole UK. So when the separatists talk about maintaining warship building in Scotland to meet the needs of a separate Scotland, they are either deluded or they are seeking to delude."
SNP defence spokesperson Angus Robertson MP said: "Under Westminster, Scotland has nuclear weapons that we don't need but not the naval vessels and marine defences that a nation with our size of coastline and strategic position should have."