The 19-year-old Australian leads the Moto3 World Championship by nine points from Alex Marquez -younger brother of MotoGP star Marc - but will skip the second tier and move straight to MotoGP next season.
Racing alongside Britain's Cal Crutchlow, LCR will prepare to field two riders in the competition for the first time since their debut in 2006.
LCR team principal Lucio Cecchinello said the new campaign would be used as a "learning season" but Miller, currently with KTM, said he feels ready to become a permanent MotoGP fixture.
"I'm very happy to make the leap up to MotoGP next year, especially because I will do so alongside Honda Racing Corporation," he said.
"It's a dream come true. I think that every rider would like to race at the highest level in the World Championship with a Honda. It is certainly a big jump from Moto3 to MotoGP, but I am convinced that we are ready and that, step-by-step, learning every day, we can do a great job.
"It's a fantastic opportunity and I'm very excited about starting this new stage of my career with HRC, whom I wish to thank together with CWM LCR Honda Team.
"I'm looking forward to working with them! In the meantime, I remain fully focused on this season's Moto3 World Championship.
"I will have to avoid any distraction in order to fight for the title."
There are five Moto3 races remaining this season, starting with the Aragon Grand Prix later this month.