To ensure the performance of the optical system, the machining accuracy of lens with long focal lengths is required to ensure the image quality. A new method for lens transmission wavefront power spectral density (PSD) in mid-frequency domain measurement using binary phase computer-generated hologram (CGH) is presented. This technique is widely applicable and is particularly useful for measuring large-size lenses with long focal lengths. A comparison experiment of the CGH measurement with results from a Fizeau sphere interferometry method is carried out to verify the accuracy and convenience of the measurement. Furthermore, measurement uncertainty due to CGH fabrication process is analysed. Analysis of the CGH test showed the overall accuracy of less than 1 nm RMS for a sphere lens with over 30 m focal length and Φ410 mm clear aperture. CGH can provide reference spheres with high precision, in the meantime greatly shorten air space, thus reducing the effect of vibration and air turbulence, therefore is of great importance for lens transmission wavefront PSD measurement. The realization of high precision, high efficiency and nondestructive testing of long focal-lens wavefront PSD ensure the ultra-precision and certainty level of machining, hence improving the comprehensive performance of the optical system.