In recent years, the fringe projection profilometry (FPP) technique has shown great prospects in the field of dynamic 3D measurement of microscopic surface shape. However, under dynamic conditions, it is desirable to use fewer projected patterns to minimize the sensitivity to motion. The commonly used phase-shifting method needs at least three fringe patterns to retrieve the wrapped phase, which depends heavily on the high-speed hardware to alleviate the effect of motion. Besides, to achieve an unambiguous measurement, at least two wrapped phase maps are required to obtain the absolute phase map, resulting in six pattern projections. In this paper, we propose the marker-embedded Fourier transform profilometry (MEFTP), which extends the modified Fourier transform profilometry with two embedded markers suited to assist the phase-unwrapping process. Combining the embedded markers with temporal phase difference information, the absolute phase can be reliably reconstructed with only two projected patterns. Furthermore, since the phase information is only encoded within a single high-frequency fringe, MEFTP is more suitable for measuring fast-moving or surface-changing objects compared with the phase-shifting method. Experiments on both static and dynamic scenes are performed, verifying that our method can achieve an accurate and robust measurement of a vibrating diaphragm at the speed of 200 frames per second.