Jones became active in the Democratic Party politics and served as a delegate to the Democratic National Convention in 1880, 1896, and 1900. He was elected to thirteen consecutive Congresses beginning in 1891.
He is best remembered as the House sponsor of the Jones Act or the Philippine Autonomy Act, which promised ultimate independence to the Philippines. Jones argued that it was beneficial to the United States to grant independence to the Philippines, as the costs of maintaining and defending the Philippines exceeded the economic benefits of possessing the islands.