Fresnel incoherent correlation holography is a new technology which can record incoherent object holograms and has important applications in biomedical imaging and 3D remote sensing. The problem of image fusion registration in hyperspectral imaging, three groups of double lens phase masks with constant focal lengths at 492 nm, 562 nm and 672 nm were designed and fabricated. The spatial light modulator called the masks of three wavelengths in turn and recorded the holograms of the objects under the corresponding wavelengths, which owed to the spatial light modulator were programmable. Because of the three-color recorded light was modulated by the corresponding wavelength mask, the spot position size of the CCD surface was the same. The reconstructed images had constant lateral magnification, which could improve the image registration accuracy and avoid complicated spatial registration algorithm of spectral images. The system truly achieved high-precision registration and real-time fusion of holographic color imaging. The color 3D image obtained from the dice holograms had high color reconstruction after numerical reconstruction and color fusion.