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The conventional direction of arrival (DOA) estimation methods are performed with multiple receiving channels. In this paper, a changeling DOA estimation problem is addressed in a different scenario with only one full-functional receiving channel. A new unmanned aerial vehicle (UAV) swarm system using multiple lifted reconfigurable intelligent surface (RIS) is proposed for the DOA estimation. The UAV movement degrades the DOA estimation performance significantly, and the existing atomic norm minimization (ANM) methods cannot be used in the scenario with array perturbation. Specifically, considering the position perturbation of UAVs, a new atomic norm-based DOA estimation method is proposed, where an atomic norm is defined with the parameter of the position perturbation. Then, a customized semi-definite programming (SDP) method is derived to solve the atomic norm-based method, where different from the traditional SDP method, an additional transforming matrix is formulated. Moreover, a gradient descent method is applied to refine the estimated DOA and the position perturbation further. Simulation results show that the proposed method achieves much better DOA estimation performance in the RIS-aided UAV swarm system with only one receiving channel than various benchmark schemes.