The effect of possible modification and refining effect of Al-Cu-P-based pre-alloy combined with Fe on the microstructure and the silicon morphology change in hypereutectic Al-Si cast alloy was studied. The samples in the as-cast state were observed by optical and scanning electron microscopy with energy-dispersive X-ray spectroscopy. The 3D morphology of both primary and eutectic silicon was observed by using colour and deep etching in detail. The results showed that the AlCu19P1.4 pre-alloy (1.07 wt.%) combined with the addition of Fe (0.02 wt.%) has a significant effect on the change of the amount, size and morphology of primary Si. This is significantly refined and changes the shape from a coarse irregular star-shaped, polyhedral, or plate-like shape to a fine polyhedral shape. The average size of the primary Si is reduced by about of 78 % from 135 μm to 28 μm and the number of primary Si particles increased from 7.4 to 237. No change in the morphology of the eutectic Si was observed; a refinement of the structure from a coarse needle/plate-like to a fine plate-like structure was seen. The depth etching method using HCl was very effective in the study of the 3D silicon morphology observed, which could be observed in detail without the presence of artefacts.