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A new three-dimensional microwave holographic imaging technique is applied for the short-range targets. It is based on two-dimensional short-range microwave holographic imaging technique by implementing Fourier analysis of the broadband reflection and transmission signals recorded by two antennas scanning together along two rectangular parallel apertures on both sides of the inspected region. The Green's function and incident field are obtained from either direct measurements or simulations. The reconstructed three-dimensional images of the target are composed of a series of two-dimensional slice images at all expected range locations. The errors induced by the three-dimensional inverse Fourier transform are reduced and the imaging quality is improved. A method of the imaging algorithm implementation has been proposed. It first uses electromagnetic computing software to establish simulation model, and obtain the incident field, the scattered field and the Green's function data of the target. Then these data are applied into the developed imaging algorithm to reconstruct target. The simulation results indicate that the three-dimensional short-range microwave holographic imaging algorithm could reconstruct the target clearly. Simultaneously, the results validated the accuracy of the proposed implementation method. Finally, we also proposed a design of a practical imaging experiment system scheme.