Train passengers were about their experiences over the previous 12 months as part of research carried out between October and November 2017 for an annual rail survey run by consumer champion Which?.
Southern, which is run by Govia Thameslink Railway (GTR), registered the lowest score nationally of just 28 per cent, an improvement from the 21 per cent the year before.
It scored just one star out of five for value for money, reliability and punctuality, and was rated two stars in every other category, while more than a third of Southern commuters, 37 per cent, thought the service had become worse in the past year.
GTR also runs Gatwick Express services, which scored 58 per cent, and Thameslink & Great Northern trains, which finished third bottom with a 39 per cent customer score.
A spokesman for GTR said: “Much of the disruption on Southern Railway has been caused by union opposition to our modernisation programme which is being carried out to transform services on the most congested routes in the country.
“The Which? analysis fails to take into account the unique and complex challenges that face GTR compared to other train operators. Southern also operates a commuter service of over 2,200 services a day and is compared with other firms which operate far fewer trains and, in many cases, operate on long distance leisure routes.
“Services are improving and we will introduce an enhanced train timetable in May to give passengers better reliability on Southern and a greatly expanded Thameslink network, creating 35,000-40,000 more seats into London.
“We have already replaced the entire Thameslink fleet and started to bring in more new trains to our Cambridge and Peterborough route, from where, in just four months’ time, we’ll have new direct cross-London services to Gatwick and beyond.
“The majority of delays are outside our control but Network Rail is investing £300m to improve reliability of the infrastructure.
“As operators of the UK’s largest rail franchise, accounting for more one fifth of all UK rail journeys, we are confident that our trailblazing achievements will be felt by rail travellers for generations to come.”
The RMT union has held 39 days of strike action since April 2016 in its fight against the further extension of driver-only operation on Southern services.
Train drivers’ union ASLEF also held walkouts in late 2016 and early 2017, and called a ban on overtime working last summer until it agreed a deal with GTR in late 2017.
Alex Hayman, managing director of public markets at Which?, said: “Fares are going up but frustrated and long suffering passengers affected by seemingly never ending delays, cancellations and dirty trains don’t feel that their services are getting any better.”