Magnesium oxysulfate (MOS) cement is an ecological inorganic cement-based material. It has several excellent properties, such as high-volume stability, light weight, low thermal conductivity, and high temperature resistance. In this study, the influences of MgO: MgSO4: H2O molar ratio on the mechanical properties and water resistance of modified MOS cement incorporating citric acid were investigated, and the change of pore structure and phase compositions were analyzed by mercury intrusion porosimetry (MIP), X-ray diffraction (XRD) and thermogravimetric (TG) analysis. The results show that when n(MgO) : n(MgSO4) or n(MgSO4) : n(H2O) is larger, the compressive strength and flexural strength of MOS cement paste increase. With the increase of MgO mole number, the softening coefficient of compressive strength decreases, while the softening coefficient and volume shrinkage of flexural strength increase. The total porosity and the most probable aperture of paste with n(MgO): n(MgSO4): n(H2O) = 8:1:20 are the largest, and smaller molar number of MgO or larger the mole number of H2O correspond to higher pore structure parameters of cement paste. In addition, with the increase of n(MgO) / n(MgSO4), the peak intensity of 517 phase is higher, while that of Mg(OH)2 is relatively weak. The content of 517 phase in MOS cement paste with the molar ratio of 10:1:16 reaches the maximum.