The Institute of Fiscal Studies (IFS) said in a new report that declining North Sea oil revenues would contribute to a £5.9 billion black hole in the country's finances.
Based on Holyrood's current budget, the IFS warned Scottish ministers would have to slash £2.5 billion from public services to match planned UK Government cuts from 2016 to 2018.
But it warned that falling oil revenues would blow an additional £3.5 billion hole in an independent Scotland's finances, which would require further cuts or tax rises.
It highlighted transport, economic development, agriculture, housing and social services - all areas where Scotland spends substantially more per person than the rest of the UK - as possible targets for cuts.
The IFS concluded: "Spending on public services higher in Scotland, but may face greater cuts under independence."
The report found spending on public services in Scotland was £7932 per person 2011/12, the most recent year for which figures are available.
The figure was 17% higher then the rest of the UK, where £6803 was spent on services per person.
But the report revealed striking difference in priorities north and south of the Border, with similar levels of spending on health, education and public order but substantially more spent in Scotland on supporting business and creating jobs, agriculture and fisheries, transport, housing and social services.
Better Together's Alistair Darling said independence would mean high tax rises or big spending cuts.
But the SNP Government said the report acknowledged savings can be made in certain areas to reflect its policy choices "helping to strengthen Scotland's fiscal position".