The assailants barged into the house of Iftikhar Ahmad at Iqbalabad in Bemina while he was away in the local mosque to lead the pre-dawn prayers, police said.
The assailants slit open the throat of Ahmad's wife, Naseema, and two children with a sharp edged weapon, the police said.
The trio, lying in a pool of blood, were rushed to hospital when the cleric, who hails from Gurez area in Bandipora district, returned home from the mosque, they said.