Marc Wearing, 28, and Charlotte Bond, 26, have been spared jail after a court case.
Police said that, on March 25 last year, officers were called to Littlehampton Road, Salvington, Worthing, after a 'report of flies and a bad smell coming from a flat'.
On arrival, the two defendants were found to be living in 'squalid conditions', with the two children, aged between one and five years old.
According to Sussex Police, the flat was full of rotting food on kitchen surfaces, bags of human excrement on the walls, and 'many black bin bags of rubbish'.
Police said the flat was found in 'filthy, squalid and unhygienic conditions'.
Detective Constable Lindsey Van-Buiten, from the West Sussex Safeguarding Investigations Unit said: "Attending officers described the conditions as the worst they had seen in their police career, and described the overwhelming smell and tens of thousands of flies inside the flat.
"Local people who called the police even thought there must be a dead body there."
Police said the two girls were immediately taken to safety and are receiving the care and support they need.
They are both healthy and doing well, police revealed.
In sentencing the pair, Judge Christine Laing said: "It breaks my heart that two little girls were living there.
"The first thing you should have done was get help from parents or friends, but you did not."
The judge told the defendants to 'stop being selfish and prioritise children above your own needs'.
The court heard that both defendants suffered from mental health issues, police said.
They were sentenced at Lewes Crown Court on Wednesday (March 23), after pleading guilty at an earlier hearing.
Each was given a two-year sentence, suspended for two years, was ordered to carry out 300 hours community punishment and 30 days rehabilitation work, police said.
Police said Wearing was also ordered to pay £450 court costs.