To realize in-situ wavefront aberration measurement of hypernumerical aperture projection optics, a hypernumerical aperture cross-phase grating lateral shearing interferometer (HNA-CPGLSI) is proposed. To achieve high-wavefront measurement accuracy, accurate alignment of HNA-CPGLSI is essential. Misalignments of HNA-CPGLSI include collimation optics, cross-phase grating, and CCD. Misalignment of collimation optics mainly produces defocus aberration. After the CPGLSI formed by cross-phase grating and CCD is accurately aligned, the alignment of collimation optics is easy to achieve by measuring and controlling the defocus aberration. So the misalignments effects analysis and alignment of CPGLSI formed by cross-phase grating and CCD are focused. Using wave interference theory and wavefront reconstruction technique, a method to analyze the sensitivity relationship between cross-phase grating or CCD and measured aberrations is built. Misalignment effects of CPGLSI on wavefront measurement accuracy are evaluated. An experimental study on CPGLSI is also carried out. The results show that the measurement accuracy of CPGLSI after accurate alignment can reach to 3.0 mλ (1.9 nm, λ=632.8 nm ) root mean square (RMS) and repeatability can reach to 0.20 mλ (0.13 nm, λ=632.8 nm ) RMS.