The airline said it had run out of patience waiting for the Scottish Government to reduce Air Passenger Duty (APD) tax.
Glasgow Airport said it was bitterly disappointed by the move.
Chief commercial officer David O’Brien said 300 indirect jobs could be lost at Glasgow due to the move with a potential fall in around 500,000 passengers.
He said: “Sadly the weaker Scottish market is even weaker still in Glasgow which simply can’t bear the burden of APD at £13.
“This should not come as a surprise to the government, we did say that our growth in Glasgow was based on their promise to abolish APD, which morphed into a promise to half APD which suddenly has disappeared into the ether and quite frankly we don’t have any more patience.”
Mr O’Brien added: “Passengers mean jobs and around 500,000 passengers will be lost at Glasgow pressurising around 300 jobs which will probably be lost.
“The flipside is that you’re looking at around 700 jobs being introduced to Edinburgh.”
Ryanair said Brexit was also a background factor threatening Scottish tourism and the airline industry.
The airline opened a new base at Glasgow Airport in autumn 2014, one of several new bases opened across Europe that year, but it will only fly to Dublin, Krakow and Wroclaw from Glasgow in its winter 2018 schedule.
It will host 45 routes from Edinburgh including 11 new routes.
A spokesman for Glasgow Airport also hit out at APD.
He said: “Despite clear and repeated warnings from both airports and airlines about the potential impact of this policy not being implemented, we are now faced with a stark scenario that includes the loss of 20 services and a significant number of jobs.”
Scottish Finance Secretary Derek Mackay said: “The Scottish Government continues to be committed to reducing ADT by 50% by the end of this Parliament and we want to get on and deliver this.
“But this has been deferred until the issues raised in relation to the H&I exemption have been resolved to ensure that the devolved powers are not compromised.”