This paper proposed a reconstruction method for the synthetic aperture in-line digital hologram with seams. The calculated means is prefilled at the seams. By using Gerchberg-Saxton (GS) weighted phase retrieval algorithm based on the angular spectrum, the phase is retrieved and the complete complex amplitude on recording surface is obtained. The particle field detection is simulated with this method. The result indicates that the correlation coefficient between the reconstructed image and the simulated particles target image doubled in contrast to the traditional method. Therefore, the influence of information loss at the seams is effectively restrained and high-quality reconstructed image can be achieved.