The Labour peer said Barnett would "wither on the vine" as the Scottish Parliament was given more powers to raise its own finances, and would be replaced by a UK-wide formula based on need.
Devised in the 1970s by the Labour peer Joel Barnett, the formula calculates the changes to the block grant sent from Westminster to Scotland, Wales and Northern Ireland.
Under the formula, in 2012-13, public spending per head in Scotland was £10,152, or 16% above the UK average of £8788. The SNP have warned a No vote could see up to £4 billion cut from Scotland's budget, as many English MPs are keen to reform or even axe Barnett.
Addressing a Unionist gathering in Edinburgh, McConnell said the issue of Barnett would become "less and less important" as Holyrood raised more of its own money after a No vote.
He said: "The old idea that all the money comes in a block grant from London and is calculated using this old, old formula is going to gradually wither on the vine.
"The time is getting very close to a position … of having a UK-wide needs assessment and deciding how UK money is spent across not just Scotland, Wales, Northern Ireland and England, but even within England … a new way of deciding that's much more transparent and fair would come on board."
Speaking to the media later, McConnell said a new formula would not necessarily mean less cash for Scots, but would mean differences between regions, with the biggest shift in public spending from the prosperous home counties to the deprived north of England.
He also said it was "hypocritical" of the SNP to warn a No vote threatened Barnett, when the formula would end with independence.
"While over the years it [Barnett] has been really important, the reality is that at least one-third, probably half, the Scottish budget is going to be determined here in future years rather than through any formula, so I think it withers on the vine because the Scottish Parliament takes on more responsibility."
SNP MSP Aileen McLeod said: "We know MPs from each of the Westminster parties are itching to cut Scotland's budget by as much as £4bn after a No vote.
"Scotland has generated more tax per head than the UK average in each of the last 33 years, and the 2012 Scotland Act would only increase Scottish control of revenues from 7% to 15%.
"The change from the Barnett Formula that Scotland needs is to control 100% of our tax and spending, which only a Yes vote delivers."
Yes Scotland yesterday launched an appeal aimed at the 160,000 European Union migrants living in Scotland.
Deputy First Minister Nicola Sturgeon said that with David Cameron promising an in-out referendum on EU membership in 2017, a No vote could see Scotland ripped out of Europe by anti-EU sentiment south of the Border.