Mesocrystals, non-classical crystalline nanostructured materials composed of aligned nanoparticles, present considerable potential for use in various engineering fields. Nevertheless, their formation mechanism and methods for size and morphology control remain unclear. For this study, the mesocrystal formation process under hydrothermal conditions was first observed for l-glutamic-acid-modified cerium oxide nanoparticle clusters using a flow reactor system which was able to control the reaction time to within 1 s. At reaction times of less than 1 s at 548 K, spherical agglomerates composed of truncated octahedral nanoparticles with random orientations were observed. Such spherical agglomerates altered their shape to cubic assemblies with an ordered superstructure as the reaction time proceeded to 8.0 s. Observations made using HRTEM and cross-section SEM with EBSD confirmed the evolution from spherical polycrystals to cubic mesocrystals. The mesocrystal formation process was analogous to conventional crystal formation and growth, where primary nanoparticles act as monomers to form an ordered structure via non-ordered agglomeration. Based on the idea that organically modified nanoparticles behave similarly to monomers in conventional crystallization, mesocrystal size control was achieved by varying the primary nanoparticle concentration and the affinity of the solvent towards the nanoparticles.