The National Maritime Museum Cornwall in Falmouth said it was "an opportune time to restructure".
A spokesman said the equivalent of three full-time jobs out of 34 staff would be lost and a new head of commerce appointed.
The museum opened in 2002 with funding from the Heritage Lottery Fund and the now defunct South West Regional Development Agency.
Richard Doughty, museum director, said: "Despite record-breaking visitor numbers this year and the strongest financial performance ever, we still carry a financial deficit."
Mr Doughty said the entire arts and museums sector in the UK "continues to go through difficult times".
According to the Charity Commission website, the museum had an income of around £2.27m in 2014-15 compared to a spend of around £2.56m.
A £21.5m maritime museum is shedding jobs despite record visitor numbers.