Nanocrystals have emerged as cutting-edge functional materials benefiting from the increased surface and enhanced coupling of electronic states. High-resolution imaging in transmission electron microscope can provide invaluable structural information of crystalline materials, albeit it remains greatly challenging to nanocrystals due to the arduousness of accurate zone axis adjustment. Herein, a homemade software package, called SmartAxis, is developed for rapid yet accurate zone axis alignment of nanocrystals. Incident electron beam tilt is employed as an eccentric goniometer to measure the angular deviation of a crystal to a zone axis, and then serves as a linkage to calculate the α and β tilts of goniometer based on an accurate quantitative relationship. In this way, high-resolution imaging of one identical small Au nanocrystal, as well as electron beam-sensitive MIL-101 metal-organic framework crystals, along multiple zone axes, was performed successfully by using this accurate, time- and electron dose-saving zone axis alignment software package.