We demonstrate local crystal structure analysis based on annular dark-field (ADF) imaging in scanning transmission electron microscopy (STEM). Using a stabilized STEM instrument and customized software, we first realize high accuracy of elemental discrimination and atom-position determination with a 10-pm-order accuracy, which can reveal major cation displacements associated with a variety of material properties, e.g. ferroelectricity and colossal magnetoresistivity. A-site ordered/disordered perovskite manganites Tb(0.5)Ba(0.5)MnO(3) are analysed; A-site ordering and a Mn-site displacement of 12 pm are detected in each specific atomic column. This method can be applied to practical and advanced materials, e.g. strongly correlated electron materials.