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Small Unmanned Aerial Vehicles (UAVs) have been proposed for use in a variety of areas including hazard analysis, disaster monitoring, agricultural mapping, and so on. Currently, the development of flight control systems (FCS) for small UAVs is complicated, time-consuming and error-prone. To address these challenges, we present a reconfigurable flight control system architecture (RFCSA) for small UAVs. RFCSA allows rapidly integrating hardware modules and verifying control laws. It utilizes a modular-based framework, in which implementation details of a typical function are packaged into a function module. In addition, each function module in RFCSA is stand-alone with its own processors, memories, power conversion and communication interfaces. In this way, the system designer could be able to focus on the system implementation, rather than pay much attention to the design details of low-level functions. Moreover, an event-driven Service-Oriented Architectures (SOA) is proposed to minimize the coupling between modules and improve the performance of inter-module interactions. The paper is organized as follows: Firstly, the challenges and requirements for small UAVs' flight control systems are discussed. Secondly, the hardware architecture based on modular concept is developed. Thirdly, event driven SOA is proposed, and the mechanisms for modules to share information and coordinate activities are introduced. Finally, the conclusion and future work is pointed out.