The invention discloses a reconfigurable hardware acceleration system for extended Kalman filtering, and belongs to the field of hardware acceleration design of algorithms. According to the method, the matrix data buffer is designed on the basis of analyzing the data equivalence between matrix multiplication in the EKF algorithm, and when the reconfigurable PE array performs current matrix multiplication calculation, the matrix data buffer provides matrix data calculated by previous matrix multiplication for the reconfigurable PE array, so that the reusability of the matrix data is fully realized, and the reusability of the reconfigurable PE array is improved. According to the method, data migration between off-chip and on-chip is reduced, operation acceleration of all matrix multiplication in the EKF algorithm is realized, and energy consumption is reduced at the same time. The data symmetry and the data sparsity in the EKF algorithm are fully utilized, trigonometric function and root extraction calculation are rapidly achieved, the reconfigurable PE array is provided with FIFO, data interaction between modules is achieved on a chip, and other optimization means are adopted, so that the calculation speed is further increased.