Iranian top negotiators and deputies foreign minister, Abbas Araqchi and Majid Takht Ravanchi, held talks with Schmidt at Vienna's Palais Coburg hotel.
The EU coordinates diplomacy with Iran on behalf of the Group 5+1 (Russia, China, France, US, Britain, and Germany).
The deputy-level talks are expected to run until Friday.
Expert-level talks also kicked off in the same city on Tuesday. Iranian Foreign Ministry's Director General for the Political and International Affairs Hamid Baeidinejad heads the country's team of experts in the sessions.
Iran and the six powers have held several rounds of talks in recent months to hammer out a lasting accord that would end more than a decade of impasse over Tehran's civilian nuclear program.
On April 2, Iran and the sextet reached a framework nuclear agreement in Lausanne, Switzerland, with both sides committed to push for a final deal, known as the Joint Comprehensive Plan of Action (JCPOA), until the end of June.