The claim will be contained in an analysis paper launched by Defence Secretary Philip Hammond in Edinburgh next week.
The paper will make the case for retaining the Armed Forces with one year to go until the independence referendum.
It also aims to stress that the Army, Navy and Royal Air Force, as well as intelligence functions, are integrated across the UK and cannot easily be divided into two fully functioning parts.
An extract released by the UK Government states: "An independent Scottish state could not simply co-opt existing units that are primarily recruited or based in Scotland, as these are an integral part of the UK Armed Forces; nor could those units in themselves provide a coherent, credible and balanced force.
"Similarly, individual members of the UK Armed Forces, in whatever units they serve, could not simply be moved into the forces of a separate Scottish state.
"UK Armed Forces personnel can expect varied and interesting careers in one of the most highly regarded, technologically advanced forces in the world, providing rewarding opportunities for international and operational experience, as well as many other benefits such as training and development, and good pay, conditions and pension.
"Personnel might very well not wish to leave the UK Armed Forces to join much smaller forces, not least because of strong bonds of loyalty.
"From a defence perspective, the transition to independence would therefore be extremely complex, raising serious questions over how an operational capability for an independent Scottish state could be managed."
The 86-page report will be published just days after MPs on the Commons Defence Committee said it would be "remiss" of the Ministry of Defence (MoD) not to consider the implications of independence.
The MoD insists it is not making any preparation for a potential Yes vote next year.
While it says the British Armed Forces are deeply integrated, MoD chiefs also agree that picking it apart would not be impossible.
The Commons Defence Committee report, published last month, criticised the Scottish and UK governments for their approach to informing the public. It concluded that the SNP's proposed £2.5 billion budget for a defence force cannot be properly judged at this point.
The Scottish Government intends to publish its formal plan for independence in the coming weeks. A spokesman said: "An independent Scotland will have first-class conventional forces which will play a full role in defending the country and co-operating with international partners - but we will not waste billions of pounds on Trident nuclear weapons.
"Scotland stands to inherit a fair share of existing UK defence assets, as the UK Government has now conceded, and an annual defence and security budget of £2.5 billion will represent an increase of more than £500 million on recent UK levels of defence spending in Scotland but would be nearly £1 billion less than Scottish taxpayers currently contribute to UK defence spending.
"We have also been clear that we will retain all current defence bases, including Faslane - which will be Scotland's main conventional naval facility - and our long-term commitment will ensure continued support for jobs and local economies in all the communities around Scotland that are home to military bases."
Angus Robertson MP, SNP Westminster leader and defence spokesman, added: "At last the UK Government has been forced to concede that an independent Scotland would inherit a fair share of UK defence assets, though Philip Hammond has many questions to answer as the perpetrator of disproportionate defence cuts and redundancies in Scotland.
"Scotland stands to inherit billions of pounds worth of assets - after all, the people of Scotland paid for them. He can take this opportunity to explain why his government promised a super barracks at Kirknewton that never happened and why his predecessor said 7,000 troops would be coming back from Germany to Scotland."