The NaA zeolite nanocrystalline aggregates composed of 6 nm ultra-small were synthesized for the first time by refluxing at near room temperature and atmospheric pressure. NaA zeolite samples had been characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and N2 adsorption-desorption isotherms. The XRD of the obtained samples at different synthesis temperatures demonstrated that their crystallinity was high. Furthermore, the SEM images of NaA zeolite synthesized at 30, 40 and 60 °C showed that its particle sizes were 130, 130 and 180 nm, respectively. Moreover, the TEM images confirmed that the NaA zeolite aggregates synthesized at 40 and 60 °C consisted of ultra-small crystals with a size of 6 nm, while the NaA zeolite synthesized at 30 °C was a single crystal. Compared with the previously reported synthetic zeolite crystals, the use of a reflux system under atmospheric pressure in this study not only synthesized the ultra-small zeolite nanocrystals (6 nm) with large specific surface area, but also avoided many safety issues brought by traditional synthesis methods under high autogenous pressure. Therefore, this study provides a precise and safe synthetic method for the development of ultra-small zeolite nanocrystals. Moreover, the large specific surface area makes them have great potential for development.