Based on the basic principle of Fourier optics and the pupil configuration of sparse aperture system, the relationship model of the thickness error between the sub-aperture and the diffractive segmented lens is established. The general expression of the phase difference induced by an arbitrary low-order surface shape error is presented under the condition of micro-deformation on one side of the sub-aperture which is without diffraction structure. Taking the spherical deformation as an example, the tolerance range of the surface shape error is discussed and calculated, and the results are verified by the ZEMAX ray tracing method. As for the special case that there is no deformation on both sides of the sub-aperture, the Monte Carlo method is used to investigate the effect of the thickness uniformity among these sub-apertures on the imaging quality of the segmented primary lens and the variance and extreme range of the sub-aperture thickness error are obtained when the coherent imaging is made by the diffractive segmented lens under a normal distribution. According to the theoretical design results, two off-axis diffractive sub-apertures are fabricated and the experiment on the segmented imaging performance of dual sub-apertures is conducted. The experimental results show that the diffractive segmented primary lens can improve the equivalent resolution.