Najwa Abu Ammar, from the southern Sweida province, said the militants didn't torture them but fed them sporadically and insulted and beat the children.
As her ordeal was about to end, Najwa Abu Ammar's 8-year-old was shot by IS militants during an operation by the Syrian military to liberate the hostages held since July. Her son Rafaat died in her arms.
His cousin Qusay, 13, was also shot and bled for five hours before he died.
"I am very sad for losing my son and his cousin Qusay," she told The Associated Press.
Abu Ammar was captured with her two sons and daughter and 26 others on July 25, when militants of the extremist group ambushed residents and went on a killing spree that left at least 216 people dead.
It was one of the deadliest IS attacks in months, targeting the Sweida province which has been spared from the worst of the violence of Syria's seven-year-long civil war.
On Thursday Syrian state media reported that troops, after months of negotiations and military operations, liberated 19 women and children held by IS in central Syria, triggering celebrations in Sweida. News of the two children's killing came out after the hostages arrived in Sweida.
One woman had earlier died in custody and another was shot dead by the extremists as they pressed for demands. In August, a 19-year-old man was also killed in detention.
Six other hostages, two women and four children, were freed in an exchange with the government in October. Negotiations were expected to free the remaining hostages but the talks failed and Syrian troops launched a broad offensive against IS in southern Syria.
The rare attacks in the province, populated mainly by Syria's minority Druze, had included several suicide bombings by the extremists, which devastated the community and shattered the region's calm.
Nashaat Abu Ammar, Najwa's husband, said his 8-year-old son Raafat was shot dead by the extremists during the Syrian army raid to free the hostages.
"They shot him in his mother's lap," Abu Ammar told The Associated Press by phone from Sweida, his voice cracking with emotion.
He only learned of his son's killing after the former hostages arrived in Sweida.
Only hours before, Abu Ammar had told the AP: "My happiness is huge."
His joy was crushed hours later when the hostages arrived in Sweida. Among them was the body of Raafat and his 13-year-old cousin. His wife appeared very frail, he said, as the hostages were barely being fed.
"Sometimes they fed us once every two days and other times twice every day," Najwa said, adding that it was mostly just olive oil, thyme and jam.
"They didn't torture us but they insulted the children and beat them," she said, speaking after returning to her home in the village, Shibki. "Then they started threatening to kill us."
She said they didn't know of the killed hostages until they were liberated.
"They held us first in a camp then a cave and kept moving us from one place to the other," she said. "At one point we were in a car for 12 hours and we didn't know where we were heading."
She was liberated shortly before noon Thursday with the others at a heel of a desert valley in central Syria.
Russian Lt. Gen. Vladimir Savchenko said the hostages were freed by the Syrian military Thursday "in an operation directed by Russian military officers." He did not provide any details but claimed that no hostages were hurt.
He also said IS kept the hostages in brutal conditions, keeping them in pits where they could barely sit or lie down, giving them no food for days and providing no medical care.
Russia is a key ally of Syrian President Bashar Assad and wields significant power in the war-torn country.
Associated Press writer Vladimir Isachenkov in Moscow contributed to this report from.
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