The interzeolite transformation approach has been used extensively for the quick synthesis of zeolites at a lower cost. Herein, an interzeolite transformation method for the quick synthesis of co-crystalline ZSM-5/ZSM-11 (CDM-5) nanoaggregates has been developed by precisely controlling the synthesis parameters and using 1,6-hexamethylenediamine as an organic structure-directing agent. In contrast, the irregular CDM-5 zeolite block obtained from an amorphous aluminosilicate gel takes a longer crystallization time using the conventional method. Combined with the related results of characterization, UV-Raman spectra show that double 6-membered rings in the parent USY zeolite framework are broken, and an ordered aluminosilicate aggregate species (OAAS) containing 4membered rings (4Rs) are formed during the interzeolite transformation. HRTEM and SEM images demonstrate that the block OAAS is dissolved into amorphous nanoparticles, followed by converting into CDM-5 nanoaggregates. These results reveal that an OAAS is essential for the synthesis of CDM-5 nanoaggregates via the interzeolite transformation method. In addition, the CDM-5 nanoaggregate catalyst exhibits superior stability and resistance to carbon deposition in the alkylation reaction of benzene with ethanol compared with the irregular block CDM-5 catalyst.