The first elements of the investigation point to a suicide, the source said, after emergency services found Jean-Michel Lambert dead at his home near Le Mans late on Tuesday.
Le Parisien newspaper reported the 65 year-old had been found with a plastic bag over his head.
Lambert had been the first magistrate in charge of the investigation over the 1984 killing of four-year-old Gregory Villemin, whose body was discovered, bound hand and foot, in a river.
The murder, which remains unsolved, was followed by a revenge killing, and by other highly-publicised twists and turns where relatives were one after the other accused of being guilty amid a series of anonymous letters.
The case was reopened several times over the past decades, and in June this year the case raced back into the headlines as a couple in their 70s and a 48-year old woman, all relatives of the child, were placed under investigation.
Judge Lambert, who was 32 at the time, was often criticized for the way he handled the case between 1984 and 1987.
On Tuesday, a French news channel published what it said were notes from another judge who investigated the case and had severely criticized Lambert's work.
A month after the Gregory's death, Bernard Laroche, a cousin of the child's father, was charged based on evidence provided by his sister-in-law, Muriel Bolle.
He was later freed after evidence against him was thrown out by prosecutors. But convinced that he was the murderer, Gregory's father Jean-Marie Villemin shot him dead in 1985 and served four years in jail for the act.
Gregory's mother, Christine Villemin, also became a suspect because witnesses said they had seen her at the post office on the day that one of the mysterious letters was sent. She was later cleared.