After the three-dimensional self-affine fractal random surface simulation, we use the optical scattering theory to calculate the deep Fresnel region speckle (DFRS) under consideration of the more strict shadowing effect. The evolution of DFRS with the scattering distance and the intensity probability distribution are studied. It is found that the morphology of the scatterer has an antisymmetric relationship with the intensity distribution of DFRS, and the effect of micro-lenses on the scattering surface causes the intensity probability distribution of DFRS to deviate from the Gaussian speckle in the high light intensity area.