Hierarchical ZSM-5 was successfully prepared using l-carnitine and l-lysine as mesoporous templates, and the influence of the dosage of “secondary template” represented by l-carnitine on the formation of hierarchical zeolite was investigated in detail. Powder X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), nitrogen adsorption-desorption, nuclear magnetic resonance (NMR), thermogravimetric-derivative thermogravimetry (TG-DTG), pyridine infrared and temperature programmed desorption of ammonia (NH3-TPD) were used to characterize the structural and textural properties of the as-prepared samples. The results showed that the hydrophilic property of the amino acid template overcame the phase separation and constructed a mesoporous system with an ultra-small size of 2–10 nm in the as-synthesized zeolite crystals. Not only the morphology and grain size, but also the Si/Al ratio and then the acidity of zeolite were affected by the “secondary template”. Catalytic cracking of triisopropylbenzene was chosen as a probe reaction so as to investigate the effect of the fabricated hierarchical porous system on the catalytic performances of the catalysts. The results showed that the introduction of hierarchical pores elevated the external surfaces of the catalyst and therefore significantly improved the catalytic cracking performance of the catalyst for the heavy molecules triisopropylbenzene. At the same time, the introduced mesopore structure also gave the macromolecule reactant a hierarchically cracking process because of the acid active sites located in the different spaces.