Virgin, which runs the West Coast main line and CrossCountry high-speed services, is cutting the number of trains that accept Saver, Supersaver and cheap day returns from 3 January.
Passengers on peak-time trains will have to buy the more expensive standard or first class tickets. A London to Manchester return ticket will cost pounds 108. A Supersaver was pounds 39.50 and a Saver was pounds 46.50.
The company is also tightening its Virgin Value ticket to force passengers to book three working days in advance instead of the current deadline of 6pm on the day before travel.
Virgin said the changes were designed to encourage people to travel on the less crowded off-peak trains and to book.
Jonathan Bray, of the campaign group Save Our Railways, said: "This latest move by Virgin will make rail travel more complicated and expensive for passengers. If rail is to compete effectively with the car it needs to be convenient and flexible."
The policy was a sign that Virgin is aiming at the business travel market at the expense of the leisure passenger, he said. "It is another indication that the long distance companies are moving towards airline fares which means that if you want to travel, book in advance - otherwise travel when they want you to," he said.
The new rules apply to trains between London and Birmingham, Manchester, Liverpool, Preston and Wolverhampton. The change also affects trains on the CrossCountry network of services that do not stop in London.
A Virgin spokesman said: "We are very anxious to reduce overcrowding wherever possible and we are trying to encourage as many passengers as possible to get a guaranteed seat by booking in advance."