Thorpe, the greatest Olympian his country has ever known, finished more than two second behind fastest qualifier Kosuke Hagino of Japan - and 13th overall.
Fellow Australians Christopher Wright, Sam Ashby and Andrew Lauterstein fared better than their team-mate and all three managed to qualify.
It was the returning Thorpe's third failure at the Chinese meet, following on from disappointment in the 100m individual medley and the 100m freestyle.
He is expected to contest to the same three events in Tokyo later this week as he gears up to the Olympic trials in March.
"If I get to the end of Tokyo and I'm not swimming faster I am going to be very frustrated and I'll be quite annoyed, because I expect this of myself at the moment," Thorpe said.
He added: "I guess putting yourself out there and racing like this is not good for your ego - but I'm comfortable with that.
"It was about the same time as I swam in Singapore (comeback meet last week) so I am happy with how I technically put the race together.
"This World Cup has definitely been tougher mentally than it has been physically."
Multiple Olympic butterfly champion Geoff Huegill and Australian Olympic boss John Coates were quick to rally around Thorpe after the sluggish start to his comeback.
"You've got to remember he's been a sleeping giant for years, to all of a sudden switch back on takes time," Huegill told Fox Sports.
"Speaking from my own experience it took a good six to eight months of competition before I started falling into the groove."
Coates said: "They're being naive - you can't just come back and in your first outing be racing as good as you ever did.
"It's going to take some time and I'm a great supporter of what he's trying to do.
"(You have got) 37-year-old gold medallists, so it's quite possible."
In the women's field, Libby Tricket, another Australian on the comeback trail, qualified fifth fastest in the 100m freestyle with compatriot Cate Campbell, quickest overall.
Swedish veteran Therese Alshammar claimed victory in the women's 100m butterfly, seeing off the challenge of Olympic gold medalist Liu Zige and world champion Jiao Liuyang in a time of 55.76 seconds.
The celebrated Chinese pair were also upstaged by promising young compatriot Lu Ying, who took silver, with Jiao settling for bronze.
"I'm not in good shape since Shanghai Worlds. I'm focusing on aerobic exercises, hoping tomorrow's 200m would be better," said Liu.
Another Chinese, Zhao Jing, asserted her authority in the women's 50m backstroke, the world record holder winning gold ahead of Australia's Rachel Goh and Gao Chang.