Set to begin in the role in the final week of February, Comyn joins from Commonwealth Securities, where he was managing director.
Comyn replaces Tom Burns, who will continue to work with the group in the United States.
"We are delighted that Matt is joining us to lead the continued development and growth of Morgan Stanley Smith Barney in Australia," Morgan Stanley Australia chief executive Steve Harker said.
Morgan Stanley assumed management control of Morgan Stanley Smith Barney in June last year and is undertaking a comprehensive development plan for the business in Australia.
The plan had also resulted in a significant number of financial advisers joining the firm, the group said.
Commonwealth Bank of Australia general manager of credit cards Stephen Karpin would take over Comyn's role from March 1, a company spokesperson said.
