The phase shift digital holographic micromeasurement system based on Liquid Crystal Spatial Light Modulator (LCSLM) is simple and easy to operate. However, LCSLM has problems of spatial inhomogeneity and edge field effect, resulting in phase distortion after modulation. To improve the measurement accuracy of phase shift digital holographic microscopy system based on LCSLM, a method of phase shift digital holographic measurement with secondary phase calibration is proposed in this paper. Firstly, based on the Fizeau interferometric system, the relationship between the gray level and the phase shift of the reflection LCSLM was calibrated once, and the phase of the distorted wavefront was measured. Then, two dimensional image interpolation algorithm and grayscale algorithm are used to design distorted phase conjugated grayscale image with the same resolution as LCSLM. Finally, the conjugated grayscale map is loaded on the LCSLM to obtain the ideal modulation phase, and the purpose of the second phase calibration is achieved. The experimental results show that after the second phase calibration, the PV value of LCSLM wavefront difference decreases from 0.182λ to 0.088λ, and the RMS value decreases from 0.039λ to 0.022λ. The overall liquid crystal surface modulation effect is more close to the ideal value, which proves that the proposed method can effectively improve the phase modulation accuracy of LCSLM. The phase shift digital holography micromeasurement system based on LCSLM was constructed, and the measurement experiment of the microlens array was carried out. The results show that under the condition of without using additional noise filtering, calibration before measuring wave of serrated fluctuation, calibration of measuring wave is relatively smooth, the micro lens array longitudinal secondary calibration rise of relative measurement error reduced to 1.15% from 3.08%, which proves that the method can effectively improve the accuracy of measurement of phase shift digital hologram. It can be seen that the precision of phase reconstruction can be controlled by using liquid crystal devices in the interferometry device, and the calibrated LCSLM has strong wave-front control ability, and significantly improved phase images can be obtained. Compared with the traditional mechanical moving phase shift measurement technology, this technology has convenient operation and simple device. Only LCSLM is controlled to change the loading pattern, and data acquisition is faster, reducing the requirements for environmental and other experimental conditions. It can be applied to deformation analysis and 3D measurement of micro-nano devices, so it has good research value and application prospect.