With the development of synthetic aperture radar realtime imaging system, more and more SAR imaging systems are based on FPGA. The transposition of image matrix data is one of the essential procedure of SAR imaging system, and its efficiency has been restricted the SAR realtime imaging system. This paper proposes a fast inplace matrix transposition algorithm based on FPGA. Firstly, matrix is segmented into submatrices of the same size. Secondly, an address sequence table which indicates submatrix address in pre and post transposition is calculated by computer in advance. Lastly, according to the address sequence table, submatrices are transposed on FPGA. The result of analysis and simulation shows that this algorithm occupies an extra 2% time span and 0.2% matrix space. This algorithm improves the efficiency of matrix transposition, reduces the burden of storage, which is important to the SAR realtime imaging system.