The 25-year-old has led Wales’ Capital Region on numerous occasions in recent seasons and co-captained Wales on their unbeaten tour this summer.
He succeeds Gethin Jenkins and will now head up a 10-man strong leadership group, which includes the duo, Matthew Rees, Josh Turnbull, Nick Williams, Lloyd Williams, Gareth Anscombe, Garyn Smith, Blaine Scully and Owen Lane.
Cardiff Blues head coach John Mulvihill said: “Ellis is one of the outstanding leaders within our group. He leads by example on and off the pitch and that has earned the trust and respect of the entire squad.
“He has previously captained Cardiff Blues on numerous occasions, particularly at the tail end of last season and including the European Challenge Cup final.
“Having previously skippered Wales Under-20s, he co-captained the Wales senior squad in the summer, so it’s a natural progression for him to become our club captain.
“Gethin has done a brilliant job previously and he remains a key figure within our environment and leadership group.
“I’m a big believer in a horizontal rather than vertical approach to leadership. It’s important to spread the responsibility across the group, the more leaders you have the easier it is to get things right on and off the field.”
Jenkins, who progressed through the region’s age-grade system, made his senior Cardiff Blues debut in 2011 and has now amassed 97 appearances.
He admits it is a great honour to captain his home region on a permanent basis but insists normal service resumes with the leadership group continuing to play a vital role.
Jenkins said: “It’s an honour to become club captain but my role within the squad doesn’t change too much. I have captained the Blues a lot over the last couple of years when boys have been on Wales duty or injured.
“It is something I am used to and we have developed a strong leadership group. I have a lot of trust in the boys, we have so much leadership experience and more often than not it is a group decision.
“As captain you need to have the respect of the squad and you can only do that if performances are there both in games and training so that is what I will be focusing on first and foremost.”