Ian Stewart, 55, of Baldock Road, Royston, has also been charged with perverting the course of justice and preventing lawful burial in April.
A post-mortem examination is due to take place on Monday. Searches at the 51-year-old's home in Royston continue.
Mr Stewart appeared before Hatfield Remand Court on Saturday.
He was remanded in custody to appear at St Albans Crown Court on Monday.
Northumberland-born Ms Bailey created the Electra Brown series for teenagers and also wrote a blog called Planet Grief after her husband of 22 years drowned on holiday in Barbados in 2011.
She was last seen walking her pet dachshund near her home on 11 April.
It is now understood the body of the dog was also found during a search of the grounds.
Hertfordshire Police said they would not be commenting on exactly where Ms Bailey's body was discovered, or how the dog died.
In a statement released by police on Saturday, her family said: "We share with Helen's friends, neighbours and fans our shock, disbelief and sadness at the news of her tragic death.
"As a family we also stand in solidarity with those around the world who have also suffered loss under tragic circumstances.
"Helen was immensely witty and talented. We love her deeply and are immensely proud of her achievements. She is now at peace and we shall all miss her terribly.
"We wish to express our gratitude to the police as well as all those who supported us in the search for Helen in whatever way they could."
Flowers have been left outside Ms Bailey's home.
A handwritten card on one bouquet says: "Heartfelt wishes are with your family. Tragic news. From a neighbour."
Another reads: "Helen, you are now at peace at last. With love, thoughts and prayers for your family and friends xx".
The partner of children's author Helen Bailey has been charged with her murder after human remains were found at her home in Hertfordshire.