Pretty sure this is Guardians of the Lost Code 3D (2010).
Guardians of the Lost Code (Spanish: Brijes 3D) is a 2010 animated adventure film, created by Ricardo González Duprat, distributed by Videocine.
During a field trip to the history museum, the students Freddy, Atzi, and Kimo discover a giant stone disk called the Codex in the storage room they are exploring. Three of the brije within it, the deities Quetzalcoatl, Ra and Chu Jung, emerge and reveal to them that they are the three people chosen to restore the ancestral alliance between humans and brijes, an alliance that was fractured with the emergence of science and technology.
The brijes are magical animal spirits that have been in contact with human beings since the beginning of time. Every human had a brije; the human cared for his brije and vice versa. When the human turned 13, a human shaman taught both partners a bonding technique that allowed them to synchronize and transform into a warrior form, gaining extraordinary power allowing them to perform various acts of heroism. Unfortunately, with the birth of modern science and technology, this union was slowly severed as humans stopped believing in magic, leading to tragic results. The brije in the Codex created and sealed themselves within it to protect the knowledge of the warrior form bonding technique from the forces of darkness that seek it.
To fulfill their mission, the Codex presents the chosen ones with their respective brijes (Hopper, Cloko and Bri) and shows them clues that will lead them to find the missing piece of the same to activate it. With their brijes and the help of Quetzalcoatl, Ra and Chu Jung, the chosen ones begin their journey through space and time to find the missing piece of the Codex, all while fighting against the forces of darkness.
The hair colours of the three kids don't quite match, but everything else seems to. There's a boy with brown hair, named Freddy, a girl with pink hair, named Atzi, and another boy with blond hair and glasses, named Kimo.
Early on in the film, they're on a field trip to a museum when they discover a giant stone disk called the Codex in a storage room, which causes three guiding spirits, Quetzalcoatl, Ra, and Chu Jung, to appear before them. The kids are subsequently given small, animal-like companions, known as a brije. Freddy's brije, named Hopper, resembles a grasshopper; Atzi's, named Bri, a hummingbird; and Kimo's, named Cloko, a chameleon. (Kimo and Cloko already know one another though, as they used to be buddies when Kimo was about five.) Each of the kids can combine with their brije into a 'warrior form.'
You can view the scene where they discover the Codex at around the 10:37 mark in the video below, the scene where they're introduced to their brije at around the 18:19 mark, and a scene where they combine with their brije into warrior forms at around the 1:15:28 mark.
The main antagonist is Elmer, a large, grey-haired man who has a colourful bird-like brije that sits on his shoulder. Elmer recruits three kids to work for him: a black-haired boy named Spikes, a brown-haired girl named Muty, and another black-haired boy named Zejas. These kids are given brije of their own, one of which resembles a scorpion.
You can view the scene where Elmer introduces these kids to their brije at around the 21:52 mark.
An infant Chinese emperor makes an appearance at around the 32:40 mark. He's given a brije of his own at around the 43:22 mark.