The 3D film, which is nominated for two Oscars and won a Golden Globe last month, has taken more than $864 million (£527 million) around the world.
Frozen beat Despicable Me 2, Ernest & Celestine, A Letter to Momo, The Croods, Monsters University and The Wind Rises to win the main prize.The Annies are Hollywood’s top animation honours for both film and TV.
Frozen’s other prizes were in the music and production design categories, as well as voice acting for Josh Gad’s Olaf the Snowman and best directing for Chris Buck and Jennifer Lee, who also wrote the script.
Pixar won five awards, including two for Monsters University and three for an ABC special called Toy Story of TERROR.
DreamWorks Animation got three awards for its hit film The Croods, in the character animation, character design and animated effects categories.
The International Animated Film Society, which published the full list of winners on its website, also honoured several live action films including The Hobbit: An Unexpected Journey for character animation and Pacific Rim for animated effects.
Legendary filmmaker Hayao Miyazaki won a writing Annie for The Wind Rises, which he has said will be his last film.
In the TV categories, Fox TV show Futurama won best general-audience animated show, Cartoon Network’s Adventure Time was named best children’s show, while Disney’s Sofia the First was voted best show for pre-school children.
Steven Spielberg was honoured for his exceptional contribution to animation, with manga artist and director Katsuhiro Otomo also among several winners of special awards.