The Doctor has had several wives. We know that he had a family before he left Gallifrey (since he did so in the company of his granddaughter Susan). We also know that he has married River Song in "The Wedding of River Song" & Elizabeth Tudor, Queen of England, in "The Day of the Doctor". He may or may not also have married Marilyn Monroe in "A Christmas Carol". His comments to Sally Sparrow, towards the end of "Blink", hint that he may have married others, too.
The title of the episode "The Doctor's Wife", however, was figurative & referred to the TARDIS.