To create an experience of open and flowing movement for visitors, the design embraces a blend of interior and exterior open spaces. The layout draws inspiration from Maya architectural concepts—specifically, courtyards enclosed by buildings, like the Nunnery Quadrangle in Uxmal.

Exhibition halls are arranged around this central nucleus, allowing for either a continuous circuit or selective visits depending on the visitor's interests and time. As with the Maya complexes, the buildings around the courtyard feature open and level lower floors, while the upper floors are adorned with a lattice in the shape of a stylized serpent. Designed by sculptor Manuel Felguérez, this lattice references the symbolic importance of the serpent in pre-Hispanic cultures.

The courtyard is divided into two contrasting zones based on the light they receive. The first is dominated by "El Paraguas" (The Umbrella); the second features a reflecting pool that links to the Mexica Hall and evokes the lake origins of this civilization. Nearby stands a wind conch sculpture titled "The Sun of the Wind", carved by Iker Larrauri, which emits sounds reminiscent of pre-Hispanic instruments.