Her view is at odds with the Scottish Government's aim of keeping passport-free travel across the UK and Ireland.
She warned that the SNP administration's pledge to pursue "healthy population growth", outlined in the White Paper on independence, will "undermine" Tory policies south of the border.
The MP for Maidenhead said: "If the people of Scotland vote to leave the UK there would be profound changes for migration policy," she said in a speech at the Scottish Conservative Party conference in Edinburgh.
"An international border would be created where one does not currently exist. This would have implications for people travelling to visit family, go on holiday or do business, and for our economies more generally.
Buried deep in Alex Salmond's White Paper is the admission that, just like the last Labour Government, a separate Scotland would pursue a looser immigration policy.
Prime Minister David Cameron will chair a meeting of the National Security Council (NSC) today to discuss possible military action against Syria.
Ahead of tomorrow's recall of Parliament, the NSC, which includes Maidenhead MP Theresa May among its members, is expected to discuss the intelligence gathered by UN inspectors from their visit to Mouadamiya, where last week's suspected chemical weapons attack is believed to have taken place
The council will also consider whether or not to push ahead with a military strike against Syrian president Bashar al-Assad.
Mr Cameron said before the meeting that any intervention in Syria would not be about the conflict itself, but preventing the use of chemical weapons by any regime.
Theresa May has spoken of her shock after being diagnosed with a chronic illness, but insisted it will not affect her demanding political career.
The Home Secretary was diagnosed with Type 1 diabetes two months ago and must now inject herself with insulin at least twice a day for the rest of her life, the Mail on Sunday revealed. She told the newspaper:
"The diabetes doesn't affect how I do the job or what I do. It's just part of life... so it's a case of head down and getting on with it. It was a real shock and, yes, it took me a while to come to terms with it.
It started last November. I'd had a bad cold and cough for quite a few weeks. I went to my GP and she did a blood test which showed I'd got a very high sugar level - that's what revealed the diabetes.
There was weight loss but then I was already making an effort to be careful about diet and to get my gym sessions in.
"Tiredness - speak to any politician and they will tell you the hours they work. Tiredness can be part of the job. It is full on."
The MP for Maidenhead Theresa May has welcomed the Transport Secretary's announcement of new investment in the A404 at Bisham. The Government has approved a scheme costing £4.2m to alleviate congestion on the road. It would see the Bisham roundabout being converted to a crossroads with signals.
The MP, who is also the Home Secretary said: “This is very welcome news and will help to tackle congestion on the A404 at Bisham, which is a constant source of frustration to local residents. The Government is right to invest in infrastructure and to support our vital transport links.”