Earl Kimrey, 32, was taken into custody by sheriff's investigators Friday.
The sheriff's office says it is believed 3- year old Mariah Woods is dead, based on the evidence recovered in the investigation.
Neighbors say Kimrey is Woods' mom's, Kristy Woods, live-in boyfriend. She told police that she went to her room again Monday morning after 6 a.m., and she was gone. He is charged with concealing of death, obstruction of justice, second-degree burglary, felony larceny and possession of stolen property.
Kimrey is now being held in the Onslow County Detention Center under a $1,010,000 bond.
Mariah's family has been cooperating with investigators and additional charges could be filed in the case, authorities said.
The search was organized in connection with the National Center for Missing & Exploited Children.
Officials said 730 volunteers participated in a search for Mariah on Friday.
At some point in the five hours between then, she said someone abducted the child - who has a walking impediment - from her bedroom.
Searchers targeted a creek and a landfill in their effort to find a 3-year-old North Carolina girl missing since the start of the week.
Miller said that the outpouring of support from the community has been "overwhelming" and asked that residents continue to support each other "as we all grieve the life of this little girl and still focus on finding her".
On Thursday, Miller called on civilians to join law enforcement officers in the land and air search for the toddler.
The FBI says they have been sending "items of interest" to their lab in Quantico, Virginia, for priority testing in the case. "Someone just walked right up in there, grabbed the 3-year-old out of the bed, and she didn't cry, she didn't scream?" he said.
'Nobody heard anything? Four people in the house, two adults and two kids, someone just comes up and snatches the baby and walks out?', Alex Woods said. She has been missing from her home since Monday.
In a tearful television appearance on Tuesday, she said: 'Please, bring her back. They said no information is too small or insignificant when looking for the missing child.