Fourteen trains are to be lengthened on the Southeastern network and seven services are to make additional stops.
The measures, in response to passenger feedback, will provide extra options and help alleviate crowding on some of the busiest services, the firm said.
Those that have had fewer passengers than expected will have carriages cut.
In January, Southeastern increased capacity on trains to Cannon Street by 24% in response to rebuilding work at London Bridge station.
Charing Cross services are unable to stop at London Bridge until August 2016, causing higher passenger numbers on Cannon Street trains during the morning and evening peak times.
Some trains are also being diverted to Blackfriars station.
The new changes to train stock will be effective from 8 March.