The polarization‐independent liquid crystal (LC) phase modulators can greatly improve the efficiency and reduce the complexity of the optical system. However, it is difficult for the LC phase modulator to achieve both good low‐loss modulation and polarization‐independent properties. A LC phase modulator of single layer microdomain twisted structure has been proposed to achieve good polarization independence and low loss in phase modulation. However, the multi‐exposure in fabrication is difficult to realize in production process. To simplify the fabrication process, an alternate LC (ALC) mask is proposed with the alternate arrangement of twist‐nematic (TN) LC and nematic LC. The fabrication process is optimized to two steps exposure with the usage of ALC and is suitable for large‐amount‐production. The measurement results showed that the single layer microdomain twisted LC phase modulator may get very low polarization dependence, about 3.52% under 2π phase modulation depth, with low loss. The device shows good potential application in optical communication, wearable device, and display.