© 2019 SPIE. Fringe projection profilometry (FPP) has attracted considerable interests for addressing the challenge of measuring three-dimension (3D) shapes of moving objects. Compared with phase shift profilometry (PSP) which requires the capture of multiple fringe patterns and is thus only suitable for static objects, Fourier transform profilometry (FTP) is less sensitive to motion-induced errors. However, FTP is prone to the influence of background lights and variations of the surface reflectivity, which may result in less accurate measurements. There are studies aimed to reduce the measurement errors with FTP using more sophisticated processing of the fringe patterns. However, existing works focus on schemes based on single images and the correlation of the dynamic 3D shapes is largely unexplored. In this work, we present a new method that refines FTP-based dynamic shape measurements. Assuming 3D rigid movements of the targets, we propose to utilize knowledge of the motion parameters and combine the multiple height maps obtained from several FTP measurements after compensating the motion effect. Approaches for automatically combining the height information are studied. It is observed that the measurement accuracy can be improved using the proposed method and the influence due to ambient lights and reflectivity variations can be suppressed. Computer simulations are performed to verify the effectiveness of the proposed method. The proposed method can also be integrated into other FPP systems to improve the performance for dynamic object measurements.