C-axis oriented HZSM-5 nanobunches were synthesized using the combination hydrothermal synthesis method and a re-aging procedure without any type of mesoscale template. Then, the samples were characterized by a variety of physical techniques, such as XRD, SEM, TEM, N2 absorption, FTIR and XPS. Their activity was investigated via the transformation of methanol to aromatic compounds using a fixed-bed micro-reactor at 450 °C of temperature and a WHSV of 2 h−1 under ambient pressure. Good correlation was observed between the re-aging procedure and the orientation of crystalline growth, the doping effect of Zn and the surface acid sites. The final product synthesized by the re-aging procedure exhibited loose aggregation with well-ordered nanobunches along the c-axis direction, and the crystal bunches are stacked together with intercrystalline distances of approximately 3–4 nm. More doped Zn sites and weak Bronsted acid sites existed on the surface of the bunches. Due to the shortened microporous channel, open mesopores and weak Bronsted acid sites, this sample exhibited a higher catalytic activity and much longer lifetime to endure coke deposition during the catalytic conversion of methanol to aromatic compounds compared to those of the conventional microsized ZSM-5 crystal.