The independent super high-rise building weakens and reduces the cooperation of functional subsystems. Implanting aerial courtyards could improve the aerial environment of that corresponding floor and enable the plane courtyards to be stereoscopic. Constructing multiple aerial courtyard-centred functional clusters of higher floors can optimise the overall space structural relationship. The paper uses the space syntax theory to discuss how to construct holistically linked aerial courtyards in a super high-rise building and applies the Grasshopper-based space syntax arithmetic logical unit to analyse and calculate the aerial courtyard of super high-rise building in different space structure modes, and also proposes design optimisation strategies based on these analyses. The paper points out that by setting aerial courtyard between vertical transportation space and functional space, establishing a direct connection between adjacent aerial courtyards, arranging vertical transportation space dispersedly and so on, it is possible to promote vertical cooperative effect, enhance integration and intelligibility of entire space structure, and provide guidelines and foundation for the construction of vertical cities.