61-year-old Jean Francis Say was on Monday charged with two counts of murder at Empire Square.
He will appear by virtual court at Camberwell Green Magistrates Court on Monday.
Police were called to the Empire Square development in Borough at about 8.15am on Sunday.
Officers discovered the bodies of two children – a girl aged 10 and a boy aged eight. They were pronounced dead at the scene.
The incident is being investigated by officers from the Metropolitan Police's child abuse investigation command.