The pursuit of precise and efficient 3D shape measurement has long been a focal point within the fringe projection profilometry (FPP) domain. However, achieving precise 3D reconstruction for isolated objects from a single fringe image remains a challenging task in the field. In this paper, a deep learning-based frequency-multiplexing (FM) composite-fringe projection profilometry (DFCP) is proposed, where an end-to-end absolute phase retrieval network (APR-Net) is trained to directly recover the absolute phase map from a FM composite fringe pattern. The obtained absolute phase map exhibits exceptional precision and is devoid of spectrum crosstalk or leakage disturbance typically encountered in traditional FM techniques. APR-Net is intricately crafted, incorporating a nested strategy along with the concept of centralized information interaction. A diverse dataset encompassing various scenarios and free from spectrum aliasing is assembled to guide the training process. A seven-map loss calculation scheme is employed to guide the training process, of which the efficacy is proved through ablation experiments. In the first qualitative experiment, DFCP demonstrates comparable phase accuracy to ground truths with 47 fewer projected images, outperforming other three methods with mean absolute phase errors of 0.0052 rad, 0.1761 rad, 0.0169 rad, and 0.0139 rad. The second qualitative experiment and the quantitative evaluation respectively prove DFCP’s capability in high dynamic range 3D measurement and in precise 3D measurement, with sphere diameter errors of 0.0780 mm and 0.0726 mm, and a spherical centroid distance error of 0.0555 mm.