An assembly composed of multiple aerial vehicles can realize omnidirectional motion with six degrees of freedom. Such an assembly has a heavier payload capacity and better fault tolerance compared with a single aircraft. Thus, such assemblies have the potential to become an ideal platform for manipulation. This paper investigates the controller design and prototype implementation for an expandable aerial vehicle assembly (AVA). The proposed AVA is composed of multiple sub-aircraft connected together via spherical joints at their center of mass. Each sub-aircraft can rotate around the spherical joint. The system dynamics of such an AVA can be separated into a slowly varying system and a fast varying system. The design criteria for a controller for this type of AVA was analyzed based on the similarity between the slowly varying system and a fully actuated rigid aircraft. This can reduce the design procedure for the controller and increase the expandability of the AVA. The stability criteria were carefully analyzed by considering the tracking error of each sub-aircraft. As an example, the controller of the AVA was designed using trajectory linearization control on the manifold, since the configuration space of the aircraft is a non-Euclidean space. A prototype composed of three quadrotors was implemented. The real-time expandable communication protocol among the different sub-aircraft was designed based on the CAN bus. Furthermore, the software and the hardware of the real-world prototype were developed. Both simulation and real-world tests were conducted, which validated the feasibility of the control design and the software implementation for an expandable assembly containing multiple aerial vehicles.