The effect of the combination of fly ash and silica fume on the water resistance of Magnesium–Potassium Phosphate Cement (MKPC) was investigated, and the improvement mechanism was discussed based on the micro-analysis of XRD, FSEM and pore structure. The results indicate that, the physical effect of the combination of fly ash and silica fume on MKPC is dominated compared with the chemical effect because of the optimization of pore structure. The combination of fly ash and silica fume leads to higher density and later-age compressive strength of MKPCs compared to those without fly ash and silica fume under air curing and water curing, respectively. The strength retention ratios (namely water resistance) of MKPCs with the combination of fly ash and silica fume at 56days are found to be significantly higher than those without fly ash and silica fume.