In recent years, integrating structured light with deep learning has gained considerable attention in three-dimensional (3D) shape reconstruction due to its high precision and suitability for dynamic applications. While previous techniques primarily focus on processing in the spatial domain, this paper proposes a novel time-distributed approach for temporal structured-light 3D shape reconstruction using deep learning. The proposed approach utilizes an autoencoder network and time-distributed wrapper to convert multiple temporal fringe patterns into their corresponding numerators and denominators of the arctangent functions. Fringe projection profilometry (FPP), a well-known temporal structured-light technique, is employed to prepare high-quality ground truth and depict the 3D reconstruction process. Our experimental findings show that the time-distributed 3D reconstruction technique achieves comparable outcomes with the dual-frequency dataset (p = 0.014) and higher accuracy than the triple-frequency dataset (p = 1.029 × 10−9), according to non-parametric statistical tests. Moreover, the proposed approach’s straightforward implementation of a single training network for multiple converters makes it more practical for scientific research and industrial applications.