The robbers managed to overcome a sophisticated security system to steal the crown and two other pieces from the museum's permanent collection, a ring and a chalice.
Created in 1899 the crown has 1,791 precious stones and pearls donated by well-to-do Lyonese families of the day.
Each gemstone was logged last year by a team of researchers, the museum said, a fact that will help trace any of the crown's parts.
The museum, situated on a hill next to a basilica, was closed Sunday as investigations continued.
The museum displays treasures from the basilica which are representative of the work of goldsmiths in the 19th and 20th centuries.