Suffering from kidney related problems, he was hospitalised for the past few days and breathed his last this morning, family members said.
He was 77 and is survived by his five sons, five daughters and a number of grandchildren.
Representing the Benaras school of Shehnai music, he was felicitated with the Sangeet Natak Akademi Award in 2009 for his contribution to Hindustani instrumental music.
He hailed from a family of renowned Shehnai exponents from Benaras and was known for his innovative style and mastery over the classical and semi-classical and folk music repertoire.
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The musician had also played at the inauguration ceremony of Doordarshan in 1973.
A top graded artiste of All India Radio, Khan also used to teach in the ITC Sangeet Research Academy here and was active before he got hospitalised.
In 2012, he was felicitated with the 'Bangabhushan' award by the West Bengal government.
Chief Minister Mamata Banerjee expressed her deep condolences to the family.
"His death is an irreparable loss in classical music. I pray for peace to the departed soul. I convey my deep condolences to the family," she said in a message.