The Hugo director will be given the Music+Film Award in honour of his innovative use of music in his films.
Last year's recipient was Pulp Fiction director Quentin Tarantino.
Scorsese has been praised by critics over the decades for the importance of popular tunes and original scores in award-winning films like Raging Bull, Goodfellas and Casino.
He also directed a series of documentaries about rock icons, including The Band's classic concert film The Last Waltz and the Bob Dylan retrospective No Direction Home.
Scorsese has received many of the film industry's most prestigious honours since the release of his 1973 breakthrough Mean Streets.
The filmmaker has won both an Emmy and a Golden Globe and in 2007 received his first 'Best Director' Academy Award for the crime thriller The Departed.
The 17th Annual Critics' Choice Movie Awards will air live on VH1 on Thursday, January 12th at 8/7c.
Scorsese's latest movie Hugo is now playing in US and UK cinemas.
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Watch the trailer for Martin Scorsese's Hugo below: