The invention discloses a method for preparing 2,6-dimethyl naphthalene by alkylation reaction of MgAPO-11 molecular sieve catalytic naphthalene. The method comprises the following steps of: I, activating an MgAPO-11 molecular sieve; and II, mixing naphthalene with an alkylation reagent and a solvent to prepare a feed solution, and carrying out alkylation reaction on the feed solution and the activated MgAPO-11 molecular sieve catalytic naphthalene to obtain the 2,6-dimethyl naphthalene. According to the method for preparing 2,6-dimethyl naphthalene by alkylation reaction of MgAPO-11 molecular sieve catalytic naphthalene, the used MgAPO-11 molecular sieve is synthesized by adopting a conventional electric heating method or a microwave heating method; the alkylation reaction of the MgAPO-11 molecular sieve catalytic naphthalene can be used for overcoming the defects that the homogeneous catalysts including anhydrous AlCl3 and the like are difficult to separate from the product, severe in device corrosion and severe in environment pollution, so that the reaction activity and 2,6-DMN (Dimethylnitrosamine) selectivity are higher, the 2,6- / 2,7-DMN ratio and anti-carbon deposition capacity are higher. Moreover, the reaction products and the catalysts are easy to separate. Besides, the method is simple to operate and convenient for large-scale production.