Mills was elated after Bolt upset the form book to win his third 100m world title at the Bird's Nest Stadium on Sunday with a season-best 9.79 seconds.
The Jamaican ended a 28-race unbeaten run by his American rival, Justin Gatlin (9.80), while extending his head-to-head record to 7-1.
"I think this is toughest victory he's had," Mills told Reuters. "For the past two years, he's had significant challenges with his preparation plagued by intermittent injuries and unfitness and (being) unable to actually complete.
"It was a very trying time and it took a lot of skill and work and determination for him to get (to) what he was able to achieve by defending his championship."
Bolt, who had struggled for form and fitness all season, stumbled his way through the semi-finals and got nowhere close to the times that Gatlin had been posting until he surged past the American over the last 30 meters at the Bird's Nest Stadium.
"It was a lot of mental pressure and we had to do work on a lot of different things in the last two weeks or so to try and get on track," said Mills, who has been coaching the 29-year-old since 2005.
"He really showed that he was a true champion. It's not the easy ones that show your character, it's those that you can win when you are not supposed to win."
Mills disclosed that he and Bolt had decided to focus their preparations on the 100m at the expense of the 200.
The Jamaican will go for successive world championship sprint sweeps with the 200 meters final scheduled for Thursday, and his coach said they would assess their build-up to the half lap race round by round, starting on Tuesday.
"I know he was a bit sore coming out of the 100, which is understandable because the things he's missing is the kind of competitive edge that allows you to go maximum speed," Mills said.
"So we're going to see ... tomorrow will give us an indication of just how much he has recovered."
Bolt, the reigning Olympic champion and world record holder, completed the world championship sprint double in Berlin (2009) and Moscow (2013).
With his 100m triumph on Sunday, the Jamaican sprinter increased his career medal haul at the worlds to nine golds and two silvers.
(Editing by Ken Ferris/Mark Lamport-Stokes)
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