Passengers on services travelling through Argyle Street and Glasgow Central Low Level will be affected, but only those wishing to board at one of the stations.
Both stations are already busy with commuters and people coming into the city for shopping and nightlife, and many more are expected to use the services during the Games.
Those heading west from the city to stations including Exhibition Centre, Partick and Scotstounhill and beyond to Milngavie, Balloch and Helensburgh must board at Central Low Level.
Those heading east from the city to Bridgeton, Dalmarnock and Rutherglen and further afield to Motherwell, Lanark and Larkhall will need to board at Argyle Street.
Glasgow Central high level station is not affected.
First ScotRail said the changes are designed to manage the increased number of passengers during the games, between July 24 and August 3.
Passengers can still get off trains at either of the stations and only those who normally get on at either Argyle Street or Glasgow Central Low Level are affected.
Passengers boarding at other stations on the routes will not be affected.
Andy Miller, ScotRail Commonwealth Games manager, said: "With more than a million extra journeys expected on our trains during Glasgow 2014 it is essential we make these changes.
"We appreciate we are asking people to change their normal routines, but it will speed up their journey home.
"To help journeys go as smoothly as possible, we're focussing on running our biggest ever timetable during the Games, with double the number of seats on key routes.
"We will continue to work with Glasgow 2014 to provide quality customer information in the lead up to the Games."
For spectators heading to venues in the west, including the SECC, Hydro and Scotstoun they will board at Central Low Level.
Those heading to Dalmarnock for the Emirates Arena and Sir Chris Hoy Velodrome and Bridgeton for the Hockey Centre at Glasgow Green will use Argyle Street, which should be accessed from Osborne Street at the rear of the station.
There will also be queuing systems in operation at some stations during peak periods, with people asked to allow extra time for journeys.
People with accessibility needs should go to Central Low Level regardless of their destination to use the Glasgow 2014 accessible shuttle buses.
Transport bosses have looked at how other cities managed transport services at major events.
Games bosses, transport chiefs and council staff have been planning ahead to ensure people travelling to venues get there as quick as possible and the city still keeps moving.
Michael Renshaw, Director of Transport and Logistics Glasgow 2014, said: "We are getting ready to welcome up to one million additional visitors to Glasgow for the Games.
"We know this means the city will be bustling with activity come Games time and transport networks will be busier than usual.
"ScotRail's one-way-system will be hugely helpful in reducing the number of people entering stations, cutting queuing times and ensuring that people can get around as easily as possible.
"We would like to thank everyone in advance for their patience, flexibility and support in making Glasgow's Games a great experience for everyone in the city."
Stuart Patrick, chief executive of Glasgow Chamber of Commerce, said: "The city centre will remain very much 'open for business' with retailers anticipating large numbers of visitors, so novel approaches to transportation are strongly welcomed.
"Visitors and commuters will benefit from advanced preparations by transport providers, making journeys much easier."
Spectators are urged to leave their cars at home and walk, cycle or take public transport. People are also being asked to plan ahead for making their normal journeys to work across the city.
More information on how services will be affected during the games is available from. http://scotrail.co.uk/games
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