The continuous phase plate (CPP) is the vital diffractive optical element involved in laser beam shaping and smoothing in high-power laser systems. The high gradients, small spatial periods, and complex features make it difficult to achieve high accuracy when manufacturing such systems. A high-accuracy and high-efficiency surface topography manufacturing method for CPP is presented in this paper. The atmospheric pressure plasma jet (APPJ) system is presented and the removal characteristics are studied to obtain the optimal processing parameters. An optimized iterative algorithm based on the dwell point matrix and a fast Fourier transform (FFT) is proposed to improve the accuracy and efficiency in the dwell time calculation process. A 120 mm × 120 mm CPP surface topography with a 1326.2 nm peak-to-valley (PV) value is fabricated with four iteration steps after approximately 1.6 h of plasma processing. The residual figure error between the prescribed surface topography and plasma-processed surface topography is 28.08 nm root mean square (RMS). The far-field distribution characteristic of the plasma-fabricated surface is analyzed, for which the energy radius deviation is 11 μm at 90% encircled energy. The experimental results demonstrates the potential of the APPJ approach for the manufacturing of complex surface topographies.