The 17-year-old, Olympic champion over both distances in London last year, could only manage fourth in Monday's 200 final, Katinka Hosszu of Hungary taking the gold.
Ahead of the 400 final later on Sunday, the last day of racing in Barcelona, Hosszu posted the fastest qualifying time of four minutes 32.72 seconds, with Spain's Mireia Belmonte Garcia second in 4:34.64 and Ye third in 4:34.93.
"It was a smoother swim this time," Ye told reporters.
"My coach told me just to do my best and relax more because I was too nervous," she added. "I have to put up more of a fight and make sure I do it right in the final."
In heats for the men's 400 medley, American Chase Kalisz posted the fastest time of 4:11.87, with Daiya Seto of Japan second in 4:12.96 and American Tyler Clary third in 4:13.55.
There were few surprises in qualifying for the men's 4x100 medley relay final, with the United States, Australia, Russia and France quickest.
However, the French and Italian women's teams were disqualified from their 4x100 medley heats as the Americans, Australians and Chinese advanced to the final with the fastest times.
(Editing by John O'Brien)
