Microcrystalline cellulose (MCC) is one of the most important excipients due to its outstanding binding and tableting properties. Owing to the absence of high resolution characterization techniques at the single particle scale, 3D (three dimension) microstructure of MCC and its effects on formulation performance remain unexamined. The aim of this work was to establish a methodology for single particles of MCC type 102 based on synchrotron radiation X-ray micro computed tomography (SR-μCT), principal component analysis (PCA) and partial least square discriminant analysis (PLSDA). Scanning electron microscopy, SR-μCT, powders properties together with tensile strength (TS), disintegration time (DT), Kawakita plots and force/displacement profiles of tablets were measured. PCA-PLSDA was applied to evaluate the structural classification of MCC particles on the basis of 2D and 3D SR-μCT derived images. The studied MCCs were found to differ in the TS, DT, Kawakita plot and force/displacement, while box ratio and Feret ratio had major influence on the principal components, but the angle of repose, bulk and tapped density did not exhibit significantly. These findings verified that different samples of MCCs from alternative suppliers have morphological diversity when assessed at the individual particle level, which could result into variation in powder properties and tableting performance.