The incident happened in the Ashkamish district of Takhar province.
The victim, who is in her 20s, told the BBC that she did not know the reason for the attack.
Although such mutilation is rare in Afghanistan, reports of violence against women are increasing.
The woman is now in hospital in Kunduz.
Her brother confirmed the nature of the injuries to the BBC, saying his aunt had seen the results of the mutilation.
A doctor at the clinic said the victim was six months pregnant, but lost the baby as a result of the violence.
'Shaved parts of her head'
The woman says her husband attacked her without any reason with a big wooden stick, cut her hair with scissor and shaved parts of her head.
She says his mother and and her sister-in-law helped her husband to tie her up with rope and beat her from head to toe.
The Takhar provincial government's women's department provided photos of the victim, who appeared badly bruised, to the BBC.
The police commander of Takhar, Noor Muhammad Hakimi, said: "The accused is on the run." He also confirmed that a case had been opened against three people, including the husband.
Previous cases of mutilation included two incidents in which husbands cut off their wives' noses.