The effects of two kinds of organic phosphonic acids on the compressive strength, water resistance, and setting time of magnesium oxysulfate cement were explored. The phase composition and microscopic morphology of magnesium oxysulfate cement were characterized by X-ray diffraction, simultaneous thermal analysis, and scanning electron microscopy. The results show that when the content of amino trimethylene phosphonic acid (ATMP) is 0.75% (mass fraction, the same below), the 28 d compressive strength increases by 113.99%, and the softening coefficient increases by 101.86% compared with the blank group. When the content of 1-hydroxyethylidene-1,1-diphosphonic acid (HEDP) is 0.75%, the magnesium oxysulfate cement shows the best compressive strength and higher retardation effect, and the softening coefficient reaches 0.93. Compounding of two organic phosphonic acids with a total content of 0.75%, when m(ATMP)∶m(HEDP) is 3∶1, it has the best modification effect on magnesium oxysulfate cement. ［Mg(OH)(H2O)x］+ generated during the hydration of MgO and organic phosphonic acid form a stable chelate, which slows down the hydrolysis of active MgO to Mg(OH)2, thereby delaying the setting time of magnesium oxysulfate cement. The addition of organic phosphonic acid provides feasibility for the application of magnesium oxysulfate cement in practical engineering.