The Flying Ad-Hoc Network (FANET) is an important component of the 6G communication system. In order to achieve the precise positioning of unmanned aerial vehicle (UAV) nodes in a FANET when satellite navigation signals are unavailable, simple and accurate direction-of-arrival (DOA) estimation methods are required. In this paper, we propose an improved correlative interferometer method to estimate the DOAs of the UAVs in a FANET. This method adopts a uniform funnel array (UFA) configuration, which consists of a uniform circular array (UCA) and an additional element located above the center. This configuration improves the estimation accuracy for DOAs with large polar angles because it utilizes the degree of freedom in the vertical aperture. In addition, the Fibonacci sampling strategy is employed to overcome the polar clustering phenomenon exhibited by latitude–longitude sampling. Furthermore, in the interferometer, only partial phase differences are used to reduce the storage burden. When calculating the similarity function, we adopt the triangular function instead of the cosine function to improve computational efficiency. The simulation results show that the proposed UFA improves the DOA estimation accuracy by $65.56\%$ over the planar UCA for signals with large polar angles. Moreover, Fibonacci sampling improves the DOA estimation accuracy by $11.54\%$ as compared to the latitude–longitude sampling.