The methylation of 2-methylnaphthalene (2-MN) and methanol is a highly promising approach to synthesize 2,6-dimethylnaphthalene (2,6-DMN). However, it is difficult to control the target product selectivity. Herein, a series of HBEA/MTW composite molecular sieves by secondary crystallization were produced by hydrothermal method and further applied for the alkylation of 2-MN. The results showed that composite molecular sieves had higher specific surface area and porosity than mechanically mixed molecular sieves, and the secondary crystallization reduced acid amount and acid density. The composite molecular sieve performed better in the alkylation of 2-MN with methanol, improving reaction conversion and selectivity of 2,6-DMN. To further improve the catalytic performance, we used Mg to modify the pure molecular sieve. The selectivity of 2,6-DMN over 1%Mg-BEA/MTW catalyst can be further increased with the 2,6-/2,7-DMN ratio of 1.5. Therefore, the composite molecular sieves have a high potential for application in the methylnaphthalene alkylation reaction.