The move is the second recent change in the senior management of the SNB after Antoine Martin was named a new member of its governing board last week.
Moser, aged 62, will leave the bank in March 2024, the SNB said on Friday. He has worked at the SNB since 1986.
In his latest position, Moser was deputy head of the bank's second department, which oversee financial stability in Switzerland.
As an Alternate Member of the Governing Board, Dewet Moser has for many years also been involved in an advisory capacity in the decisions of the Governing Board, the SNB said.
No successor for Moser has been named, with the SNB's non-executive bank council - which oversees the central bank - making a recommendation to the Swiss government.
(Reporting by John Revill, Editing by Rachel More)
