To overcome the difficulty in 3D shape measurement of dynamic isolated scenes, this paper proposed a method of temporal Fourier fringe analysis. The temporal modulation of the multi-period phase-shifted projection fringes by the measured dynamic scene was given full play in this study. On this basis, a temporal Fourier fringe analysis was carried out on these deformed fringes loaded with information of changes in the measured surface shape. Phase extraction was then conducted, and the corresponding 3D reconstruction of the dynamic isolated scene was achieved. The spatial high-frequency information of the complex scene was well retained by this method. Meanwhile, for the accuracy and reliability of the phase information, a disc grating of three-frequency composite fringes was designed. The grating, driven by a motor, began rotation projection, producing multi-period phase-shifted fringes on the measured scene surface. No spectrum filtering operation was performed in the spatial domain. Temporal phase unwrapping was carried out after the corresponding phase information was solved for the three-frequency fringes. The proposed method is suitable for isolated object measurement. Only one frame of a deformed fringe pattern is required for the retrieval of its corresponding 3D shape, so this method is applicable to dynamic scene measurement. Verification experiments were conducted on a newly developed measurement system. The results demonstrate the feasibility of the proposed method and system.