Paul Hemming, 42, of Alderney Avenue, Milton Keynes, is accused of killing Natalie Hemming, 31, who was last seen in Hemel Hempstead, Hertfordshire, at about 15:00 BST on 1 May.
She was reported missing from her home in the Newton Leys area of Milton Keynes on Tuesday by a relative.
Mr Hemming was remanded in custody and is next due to appear in court in July.
Mother-of-three Ms Hemming, lived with her partner and their children.
Thames Valley Police said the search for her is continuing.
It is trying to trace the movements of a black Ford S Max - registration EJ12 UWG - between 21:45 on 1 May into the early hours of Bank Holiday Monday.
The car travelled towards Aylesbury on the A413, then south of Aylesbury on the A41 before returning to Milton Keynes on the A418, the force said.
A man charged with the murder of his partner who has been missing for six days has appeared in court.