Speaking at the Scottish Renewables annual conference in Edinburgh, Davey said that Scottish renewables benefit from the ability to spread investments and costs across the whole of the UK consumer base.
But if Scotland votes for independence in the planned referendum next year, the cost of subsidies would have to be borne by the much smaller base of 2.5 million Scottish consumers.
And he warned that an independent Scottish government would face "serious competition" with other countries that could supply the UK, such as Norway and Ireland, with whom the UK government is pursuing interconnection projects.
Davey said: "An independent Scotland means just that. Treated by the UK as just one of a number of countries that it could buy renewables from.
"If the UK were to look beyond its borders for renewables, we would have to consider which sources provide the cheapest and most reliable options for our people.
"I am absolutely not saying that Scotland wouldn't be able to compete. But it will be much harder to keep prices competitive."