"The Maori All Blacks team has a very strong identity with an exciting style of rugby, and special cultural base," McMillan said.
"I want to ensure that it continues to provide a pathway for players wanting higher honours.
"This is a very proud moment for myself and my family. My vision for this team is to continue to build on the legacy that has been carved out for this team.
"I want to ensure that we take a holistic approach to our work with this team; that players can play great rugby in this environment and that they can celebrate who they are as Maori."
Dr Farah Palmer, New Zealand Rugby's Maori board chair, welcomed McMillan's appointment as an exciting new chapter.
"This is really exciting for Maori rugby. We are looking forward to having Clayton lead the Maori All Blacks as he is a talented coach with a track record of developing players and developing great team culture.
"His work with the New Zealand Provincial Barbarians in the lead up to their match against the British and Irish Lions was outstanding and I expect he will bring the same strong work and cultural ethic to this special team," Palmer said.
McMillan's first task is to lead New Zealand Maori on a two-match programme in the northern hemisphere in November.