The invention discloses a method for pretreating a paraffin hydrocarbon selective isomerization catalyst. The method comprises the following steps: (1) filling a catalyst precursor containing amorphous silica-alumina I and active metal components in an upper bed of a fixed bed reactor, and filling a catalyst precursor containing amorphous silica-alumina II and active metal components in a lower bed of the fixed bed reactor; (2) introducing an aqueous solution containing organic amine and halohydrocarbon, carrying out a contact reaction with the catalyst precursor, and introducing oxygen-containing gas for treatment; (3) introducing an aqueous solution of ammonium nitrate to carry out a contact reaction with the catalyst precursor, and introducing nitrogen or inert gases for treatment; and (4) introducing hydrogen-containing gas to be activated, obtaining a catalyst with a ZSM-35 molecular sieve on the surface of the upper bed, and obtaining a catalyst with a ZSM-23 molecular sieve on the surface of the lower bed. According to the method, the distribution of the molecular sieves formed on the catalyst surface is uniform, the utilization rate of the molecular sieve is improved, the reaction selectivity and activity are improved, the cost is greatly reduced, and environmental protection is promoted.