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.
Rail services in the Thames Valley were badly disrupted again tonight because of another signal failure caused by flooding at Maidenhead. Dozens of services have been cancelled or delayed.
First Great Western say the issue which started at around 5pm has now just been resolved but delays will continue for the rest of the evening. Around half of all trains were cancelled or delayed during the rush hour.
It comes as Network Rail warn passengers delays could continue for two months because of rising water levels.
Rail services across the Thames Valley are today in chaos because of flooding hitting hundreds of thousands of passengers. By 6.30am, even before the busy rush hour got underway, more than 20 services from Reading, Oxford and Newbury had been cancelled.
First Great Western say they can't say how long the problems will last.
Only four of the usual twenty five trains an hour are running into Paddington.
Reading is by far the most badly hit but the lines to Oxford and Newbury also have very few services.
The problems are at Maidenhead where two of the four tracks can not be used and between Didcot and Oxford. This is on top of line closures in the West Country.
Passengers are advised to use Chiltern or South West Trains where possible.
Maidenhead has secured a place among the UK’s top performing towns and cities – taking seventh place ahead of cities like Bristol, Edinburgh, York and Oxford.
The UK Vitality Index – a ‘health check’ on large towns and cities outside London by commercial property consultants Lambert Smith Hampton – identifies those that have ‘healthy and robust economies, are best placed to support growth and will provide opportunities for businesses to expand’.
This confirms Maidenhead’s enviable position for business development and investment, and the prognosis is for increasing strength in the future. Our Transforming Maidenhead event last week in the House of Commons demonstrated a very healthy interest in the opportunities our town has to offer. We approach 2014 with renewed confidence in Maidenhead’s ability to contribute fully to a buoyant economic future, in the borough itself, regionally and country-wide.”
– Cllr MJ Saunders, cabinet member for planning, property and Maidenhead