The invention relates to a hydrophobic association zwitterionic polymer and a preparation method thereof. The preparation method comprises the following steps: adding acrylamide, acrylic acid and cationic monomers containing quaternary ammonium groups sequentially into a reactor; adding water and dissolving; adjusting the pH value of a system to be 6 to 9 by using NaOH; supplementing deionized water to enable the total monomer mass percentage of the reaction system to be 10 to 30%; adding surfactant lauryl sodium sulfate and stirring uniformly; adding an acrylamide hydrophobic monomers containing capsaicin functional groups; introducing N2 for 20 minutes; and adding a water-soluble initiator and performing polymerization reaction to obtain the hydrophobic association zwitterionic polymer. The positive charge content and the negative charge content of the hydrophobic association zwitterionic polymer prepared with the method are equal, a solution of the polymer has an antipolyelectrolyte effect, and the hydrophobic association zwitterionic polymer has excellent salt resistance. The introduced hydrophobic units containing the capsaicin functional groups have bioactivity and adopts a rigid benzene ring structure, so that the polymer has excellent tackifying property, temperature resistance, salt resistance and anti-microbial property, high dissolution speed and low price, and has an excellent application prospect in petroleum reservoir exploitation under the conditions of high temperature, high salt and bacteria in existence.