A compound-eye imaging system based on the phase diffractive microlens array as a compact observation module is proposed. As compared with the refractive microlens in common compound-eye imaging systems, the diffractive microlens is a flat imaging optics featuring high relative aperture, thin component thickness and compatibility with lithography techniques. As an application, a compact fingerprint imaging module was demonstrated using this compound-eye imaging system. The phase Fresnel microlens array with continuous trough morphology was fabricated via the self-developed gray-scale laser direct write equipment. An image reconstruction method is proposed by extracting the effective image information of each Fresnel microlens, removing the complex signal separator layer from the compound-eye imaging system. The illumination optics is further planarized through the waveguide backlighting and the waveguide functions as the touch panel for fingerprint recording. The novel compound-eye imaging device length was only restricted by the focal length of the microlens with a low limit of 4.12f. The applicability of this novel compound-eye imaging system was further demonstrated by recording the human fingerprint texture, paving ways for various applications as a compact imaging system.