Abstract: In order to improve the hydrophobic properties of coral aggregate mortar, a hydrophobically modified mineral powder was prepared by modifying mineral powder with polydimethylsiloxane (PDMS). Based on Modified Andreasen-Andersen (MAA) model and the response surface method, the mortar mix ratio was designed, and a hydrophobically modified coral aggregate mortar was developed. The effects of individually incorporating PDMS, individually incorporating hydrophobically modified mineral powder, and a combined addition of PDMS hydrophobically modified mineral powder on the hydrophobic properties and mechanical properties of the mortar were compared and analyzed. The hydrophobic mechanism was studied using X-ray diffraction, Fourier transform infrared spectroscopy and scanning electron microscopy. The test results show that the hydrophobically modified mineral powder was prepared using a PDMS content of 5%. The mix with 5% PDMS and 10% hydrophobically modified mineral powder showed excellent hydrophobic properties, achieving a contact angle of 123.4° and a water absorption of 0.16% after 8 h. Compared to the blank group, the compressive strength of the 5% PDMS group decreased by 37.7%. In contrast, the strength of the 10% hydrophobically modified mineral powder group increased by 14.5%, while that of the combined (5% PDMS + 10% powder) group decreased by 39.2%. PDMS improves the hydrophobicity of the material by forming a hydrophobic film on the surface of hydrated calcium silicate, and the hydrophobic modified mineral powder cuts off the water transport path by blocking the pore connectivity, thereby achieving the hydrophobic effect. PDMS reduces the compressive strength by reducing the content of hydrated calcium silicate, while the effect of hydrophobically modified mineral powder is the opposite. The negative effect of PDMS dominates the overall compressive strength.