Herein, a phase error correction method based on a multi-level fringe order correction was proposed to address the issue of the easy generation of the phase-jump error in the multi-frequency heterodyne phase unwrapping method. First, the initial rough correction was performed on the synthetic fringe orders according to the phase period of the synthetic fringe, which can effectively avoid further accumulation and transmission of the phase-jump error caused by the Gamma effect and flooring function. Thereafter, the secondary fine correction was performed on the initial fringe orders by optimizing the flooring function and using the absolute phase of the error. Finally, a more accurate target absolute phase was calculated based on the corrected fringe orders. Experimental results showed that the three-dimensional reconstruction model corrected by the proposed method exhibited a smooth surface, clear details without obvious spots or color patches, which can significantly suppress the phase-jump error and enhance the robustness of the structural light three-dimensional measurement system.