The invention relates to a resin-based composite adsorbent for synchronously and deeply remove phosphorus and fluorine in water and a preparation method thereof. The preparation method includes: weighing resin, adding the resin into a prepared titanium tetrachloride-hydrochloric acid-anhydrous alcohol solution, stirring in constant-temperature water bath, filtering, drying, adding a prepared NaCl+NaOH solution, stirring, filtering, cleaning, rinsing, and drying; weighing zirconium oxychloride, adding into a a hydrochloric acid-alcohol-water solution, adding the resin which is dried to constant weight, stirring in water bath, filtering, drying, adding into a NaOH solution, stirring, filtering out, washing with water to neutral, using a NaCl solution and alcohol for rinsing, filtering, and drying to constant weight to obtain the resin-based composite adsorbent. A carrier of the adsorbent is macroporous anion exchange resin with quaternary ammonium functional group, and nanoparticles of titanium oxide and zirconium oxide are distributed on the surface and in pores of the carrier; the composite adsorbent has the advantages of high adsorption capacity, high selectivity and capability of synchronously removing phosphorus and fluorine and can be applied in deep phosphorus and fluorine removing treatment of drinking water and industrial wastewater.