An attitude estimation algorithm is designed by using Gaussian Particle Filtering(GPF）,algorithm.The quaternion discrete equation is taken as the state equation. The algorithm consists of five modules:sampling conditioning particle, sampling particle, weight calculation, mean covariance calculation and Cholesky. The “average” value and covariance matrix of the quaternion are calculated by using non-standardized weights, and the calculation formula of the covariance matrix is rewritten.In this way, the pipeline Gaussian particle filter algorithm is implemented. At the same time, a parallel design scheme is proposed, which can further optimize the running speed by using the remaining resources of FPGA. The simplified particle filter algorithm and Gaussian particle filter algorithm presented here can not only be used in UAV attitude estimation, but also be applied to other nonlinear estimation problems and applications. The simulation results have proved the feasibility and effectiveness of this design.