The cuts will effect services from Sunday night to Thursday night and allows maintenance and improvement work to take place.
Changes come into affect from May 21, and will not affect services on Friday and Saturday night.
A Southern spokesman said: ‘Passenger numbers have doubled in the past two decades and Network Rail needs this extra time to carry out essential maintenance and improvement work overnight to give passengers at busier times of the day a more punctual and reliable journey across the Southern network.
‘It will also help Network Rail deliver critical elements of a £300 million improvement plan that was announced by the government in January, which will improve our services on this, the UK’s busiest, most congested network.
‘Just 14 trains in total are being affected overnight into and out of London Victoria and the busy Friday and Saturday night trains won’t be altered at all.’
A Network Rail spokesman said: ‘The railway south of the capital is the busiest and most congested part of the national network, carrying almost a third of Britain’s rail passengers on a daily basis.
‘Even small delays can quickly build up into major disruption - so it’s vital we work with the train operators to tackle the root causes of those delays.
‘The changes we’ve agreed with Southern will give our engineering teams more time overnight to carry out vital maintenance and improvements, targeting known delay hotspots and delivering a better, more reliable railway for hundreds of thousands of peak-time passengers each day.’
Fresh talks aimed at resolving the year-long dispute over the role of conductors are due to be held next week.
Leaders of the Rail, Maritime and Transport union will meet with the company on May 15.
Conductors have taken 31 days of strike action in the past year in protest at changes to their role.