The temple has been designed in the lines of Nanda (Krishna's foster-father) temple, in Vrindavan. Therefore, it is also known as Nanda Bhavan or Nandalaya (the House of Nanda).

Structurally, a kalasha on the shikhara marks the top of the temple, on which seven flags are flown along with the Sudarshana Chakra. The seven flags represent the seven 'houses' of Pushtimarg or Vallabha Sampradaya. The temple is also popularly called Shrinathji ki Haveli (House of Shrinathji). With the mood of worship in Pushti Marg, Shrinathji is not seen as an impersonal God so the worship is not done like in a temple. Shrinathji is seen as Thakorji or lord of the House or Haveli and seva (service) is offered rather than worship. Like a regular household it has a chariot for movement (In fact the original chariot in which Shrinathji was brought to Singhar), a storeroom for milk (Doodhghar), a storeroom for betel (Paanghar), a storeroom for sugar and sweetmeats (Mishrighar and Pedaghar), a storeroom for flowers (Phoolghar), a functional kitchen (Rasoighar), a jewellery chamber (Gahnaghar), a treasury (Kharcha bhandaar), a stable for horses of chariot (Ashvashala), a drawing room (Baithak), a gold and silver grinding wheel (Chakki).

The Nathdwara temple has subsidiary temples dedicated to the deity Madan Mohanji and Navneet Priyaji, located in the main complex.