The action is over plans for drivers, rather than conductors, to operate carriage doors at certain times.
It is due to last until Friday morning, with a further three blocks of strikes planned before Christmas.
The RMT has said the rail company's plans put passenger safety at risk. Southern has urged the union to "move forward".
Southern said it plans to run 61% of its normal timetable, which equates to 1,373 trains.
But the rail company said fans should make alternative plans where possible for getting to and from the Brighton and Hove Albion v Wolverhampton Wanderers match at Falmer, which kicks off at 19:45 BST.
On Monday, Southern told union members a lump sum of £2,000 was back on the table if they end the dispute over conductors.
The £2,000 lump sum was originally offered if conductors accepted new contracts by 6 October.
However, the RMT said the renewed offer was a bribe and did not move the dispute on "a single inch".
A fresh three-day strike by staff on Southern rail is under way, with hundreds of trains cancelled.