The 27-year-old German, identified as Jennifer W, and her husband bought the child as a house "slave" in the IS-occupied Iraqi city of Mosul 2015.
Her husband chained the girl up outside after she fell ill and Jennifer W did nothing to save her, prosecutors say.
She also faces murder and weapons offences charges.
If found guilty in the terrorism court in the city of Munich she faces a maximum sentence of life in jail.
The five-year-old girl was among a group of prisoners-of-war when Jennifer W and her husband bought her.
German media say the child may have been a member of the Yazidi minority, many of whom were captured and enslaved by IS as the militant group swept across northern Iraq in 2014.
"After the girl fell ill and wet her mattress, the husband of the accused chained her up outside as punishment and let the child die in agony of thirst in the scorching heat," prosecutors said in a statement.
"The accused allowed her husband to do so and did nothing to save the girl."
Jennifer W travelled to Iraq in 2014, where she became a member of IS's self-styled morality police, the allegations against her say.
Her role saw her patrol parks in Mosul and another IS-occupied city, Fallujah, armed with a Kalashnikov assault rifle, a pistol and an explosives vest, prosecutors said.
"Her task was to ensure that women comply with the behavioural and clothing regulations established by the terrorist organisation," said the statement.
Jennifer W was arrested by Turkish police months after the girl's death after she visited the German embassy in the capital Ankara to renew her identity papers.
She was extradited to Germany, where she was initially allowed to return to her home in the state of Lower Saxony because of a lack of evidence against her.
German police arrested her in June as she tried to travel to Syria and she has been in custody since then.
No date has yet been set for the trial.
Mosul was liberated from IS last year after a three-year occupation and the group has now lost almost all the territory it controlled in Iraq and Syria.
Source: bbc.com