The museum is located in one of the palaces of the Red Fort, Delhi. It is believed that this palace was built by Shah Jahan for his queen Arjumand Banu Begum also famously known as Mumtaz Mahal. The objects are displayed thematically in six galleries belonging to the Mughal period.

The first few showcases have articles belonging to Emperor Akbar and his successors which include miniature paintings, manuscripts, stone inscriptions, farmans (royal orders) etc. One of the showcases has 17th century brass astrolabes which were used for astronomical calculations like measuring the distance between heavenly bodies, day and night times etc. The next gallery has porcelain, celadon and jade objects, textiles and glazed tiles. The most distinctive of the Mughal jade objects are the hilts of swords and daggers, usually plain but beautifully carved and finished. Curtains, carpets, pillows, cushions and costumes are also on display in the museum.

The Bahadur Shah Zafar gallery houses objects belonging to the last Mughal emperor Bahadur Shah and his queen like costumes, pen holder, ink pot, scissor, gun powder horns, rose water sprinkler, toilet box etc. Two specimens of calligraphy of Bahadur Shah II, an ivory miniature believed to be of Zeenat Mahal and a photograph of the last days of Bahadur Shah in the prison at Rangoon deserve special mention.

One can also find the arms used in the war of 1857 by the then Nawab of Pataudi, arms used by Bahadur Shah and field glass used by General J. Nicholson during the siege of Delhi here. Portraits of the last Mughal rulers and contemporary personalities like Mirza Ghalib, maps and lithographs depicting scenes of Delhi, Bahadur Shah's letter to Queen Victoria with the thumb impression of his son Jawan Bakht, are some of the other interesting pieces of display in the museum.