The invention discloses a magnetic silica porous adsorbent and a preparation method and applications thereof. The preparation method comprises following steps: mixing silica powder and an iron ion solution; adding a hot alkali solution with a temperature of 60 to 80 DEG C to adjust the pH; after complete reactions, cooling the solution to the room temperature, carrying out aging, washing to the product until the product becomes neutral, drying, and grinding to obtain the magnetic silica porous adsorbent. According to the preparation method, an inorganic silicon source namely silica powder is taken as the raw material, silica powder is cheap, easily-available, nontoxic, and environmentally friendly, during the preparation process, no organic waste liquid is generated, the preparation methodis environmentally friendly, a surface deposition method is adopted, one-step synthesis is performed at a low temperature, the reaction time is short, the energy consumption is low during the preparation process, and the cost is low. The magnetic silica porous adsorbent has good selectivity, the maximal methylene blue adsorption quantity is 121.23 mg / g, and the maximal malachite green adsorptionquantity is 163.52 mg / g.