The winning bidder will have one of seven main characters named after them and the proceeds will be donated to the writer's old school in Scotland, so its students can attend a Christmas show.
Millar has previously held auctions to name characters in Nemesis and The Secret Service to raise money for charitable causes.
"It's something I'd like to do every year and expand into other schemes in the community with a few other ideas I have," The Hollywood Reporter quotes Millar as saying.
"Some of the kids had never been to the city before and when I went back to my old school to hand out prizes last summer they all told me how much they enjoyed it."
Illustrated by Frank Quitely, Jupiter's Children is a multi-generational superhero epic that centres on young superbeings dealing with the burden of living up to their parents' legacy.
The series will debut through Image Comics in April next year.