Pictures from Chopper 11 HD showed deputies outside a home and a series of rundown buildings and trailers at a property about a mile from the Wayne-Sampson line.
Animal Control Director Justin Scally said in a news release sent to the media that "I can finally rest easy knowing that these animals are no longer living in constant confinement."
Because of the sheer number of animals involved in the raid, many dogs were moved to the Wayne County Fairgrounds where each animal's health was being evaluated.
According to a website for Thornton's Kennels, it specialized in smaller breeds including Lhasa Apso, Shih-Tzus and Chihuahuas.
Animal Controls workers said when they arrived at the kennel, they found the dogs "suffering from serious medical ailments and housed in filthy conditions. Many of the dogs were emaciated, had untreated lacerations, severely matted fur and serious skin and eye infections. They were being housed in unheated cages inside unventilated barns and outhouses. It was obvious that many of these animals had never known life outside their wire cages."
Investigators said they'd been examining the operation for about a year before deciding to move in.
Humane Society officials said the case shows that North Carolina needs stronger laws governing puppy breeders.
"These animals were denied basic veterinary care and socialization. This terrible cruelty could have been avoided if North Carolina had laws addressing the puppy mill industry," said Amanda Arrington, North Carolina state director for The HSUS.
Wayne County officials have not yet said what the future holds for the dogs they've seized and if they'll be put up for adoption.