The 2006 Cup of China took place at the Olympic Center in Nanjing, China. Since Emily had trouble on her combination jump in the short program at Skate America, she changed it to a triple flip-double toeloop. It gave her a clean skate for the lead going in to the free skate with 56.74 points.

Emily had some jump problems in the free skate and was 3rd place with 94.38 points. She was in 3rd place overall with 151.12 points, earning her first Grand Prix medal.

Emily Hughes skated to Carmen by Bizet in a new black dress earning 57.42 points for her short program. This year she has added a Charlotte move into a combination spin and a new flying sit spin with a twist. She had trouble with her combination jump, but kept the character of Carmen throughout her program.

She performed a nice triple Lutz-double toeloop-double loop jump in her free skate to Sylvia by L. Delibes for a score of 89.92.

Emily placed 5th in the short program, 6th in the freeskate and 5th overall with a total score of 147.34