Statistical nanoindentation technique has been widely used to study the microstructural mechanical properties of various types of hardened cement pastes, which has significantly improved the fundamental understanding on the mechanical performances of concrete and other cementitious composites. However, it was noted that the contradictory results from statistical nanoindentation technique appeared in the literatures and the critical aspects in the application of this technique to hardened cement pastes were recognized. This work is designed to provide an insight into the critical aspects, including the influences of material microstructure and statistical analysis method. Firstly, the microstructure of hardened cement pastes was investigated by SEM-BSE/EDX analysis. Then, the influence of heterogeneous material microstructure on the nanoindentation results was investigated through a micromechanical method. After that, two general methods of parameter estimation were applied to analyze the nanoindentation data and global optimal results were sought by multiple runs with the random starting values. This work revealed that the indented 'Calcium-Silicate-Hydrate' microstructure is a fact of the composites and the analysis result largely depends on the selected statistical analysis method. The influences of material microstructure and statistical analysis method may cause unreliable result. In this paper, a method for the verification of the result from statistical nanoindentation technique in hardened cement pastes was proposed.