Abstract: In order to improve the hydrophobic properties of coral aggregate mortar, hydrophobic modified mineral powder was prepared by modifying mineral powder with polydimethylsiloxane (PDMS). Based on Modified Andreasen-Andersen (MAA) model and response surface method, the mortar mix ratio was designed, and hydrophobic modified coral aggregate mortar was developed. The effects of single-doped PDMS, single-doped hydrophobic modified mineral powder and PDMS+hydrophobic modified mineral powder on the hydrophobic properties and mechanical properties of the mortar were compared and analyzed. The hydrophobic mechanism was studied based on X-ray diffraction, Fourier transform infrared spectroscopy and scanning electron microscopy. The test results show that the hydrophobic modified mineral powder used in the test is modified by PDMS with a content of 5%. The 5% PDMS+10% hydrophobic modified mineral powder group showed excellent hydrophobic properties, with a contact angle of up to 123.4° and water absorption of 8 h is 0.16%. Compared with the blank group, the 5% PDMS group and the 10% hydrophobic modified mineral powder group, the compressive strength decreased by 37.7%, increased by 14.5% and decreased by 39.2%, respectively. 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 of hydrophobically modified coral aggregate mortar by reducing the content of hydrated calcium silicate, while the effect of hydrophobically modified mineral powder is opposite. The negative effect of PDMS dominates the compressive strength.