Aurangzeb briefly sequestrated the state (c.1679) on the pretext of a minority, but the rightful ruler Maharaja Ajit Singh was restored to the throne by Veer Durgadas Rathore after Aurangzeb died in 1707 and a great struggle of 30 years. The Mughal empire declined gradually after 1707, but the Jodhpur court was beset by intrigue; rather than benefiting from circumstances, Marwar descended into strife and invited the intervention of the Marathas, who soon supplanted the Mughals as overlords of the region. This did not make for stability or peace, however; 50 years of wars and treaties dissipated the wealth of the state, which sought and gratefully entered into subsidiary alliance with the British in 1818.

During the British Raj, the state of Jodhpur had the largest land area of any in Rajputana. Jodhpur prospered under the peace and stability that were a hallmark of this era. The land area of the state was 23,543 sq mi (60,980 km2) its population in 1901 was 44,73,759. It enjoyed an estimated revenue of 35,29,000/. Its merchants, the Marwaris, flourished without let or limit and came to occupy a position of dominance in trade across India. In 1947, when India became independent, the state merged into the union of India and Jodhpur became the second city of Rajasthan.

At the time of partition, ruler of Jodhpur Hanwant Singh did not want to join India, but finally due to the effective persuasion of Sardar Vallab Patel, the then Home Minister at the centre, the princely state of Jodhpur was included in Indian Republic. Later after State Reorganization Act, 1956 it was made part of the state of Rajasthan.