Abstract At the microscopic scale, fresh cement paste is composed of random packing of irregular cement particles and their packing behavior plays an important role in microstructural evolution. The preponderance of previous work has focused on the microstructural model by random packing of spherical or two-dimensional (2D) elliptical particles, and little is known about three-dimensional (3D) ellipsoidal particles. In this paper, based on the geometric model of ellipsoid, the previous work on the contact detection algorithm of ellipses is extended to ellipsoids. According to a modified cement particle size distribution function, the microstructural model of fresh cement paste is constructed. Applying stereological tools and serial sectioning analysis technique, the influence of cement particle shapes (oblate, spherical and prolate) on the microstructure of fresh cement paste is presented. Moreover, the reliability of the statistical results is verified by valid experimental and theoretical results.