Graham, who knew the pastor who was killed in the tragedy, said his niece went to 8th grade and high school with suspect Dylann Roof.
According to the senator, his sister Darline told him about his niece Emily going to school with roof.
"Emily said that in school he was just a quiet, strange kid," Graham said on ABC's "The View" Wednesday morning. "Seems like one of these Newtown type guys," referring to the Connecticut massacre.
After news broke overnight of the deadly church shooting that took nine lives, Graham joined ABC's "The View," which he was previously scheduled appear on before the tragic events in his home-state unfolded.
"I can’t explain this," he said. "I don’t know what would make a young man at 21 get so sick and twisted to kill 9 people in a church – this is beyond my understanding."
Graham said he thinks it was probably a number of factors that led to the young man to open fire during the Bible Study class.
"There are real people out there who are organized to kill people in religion and based on race," Graham said. "But it’s 2015 there are people out there looking for Christians to kill them. So this is a mean time we live in."