Using template-containing silica microspheres as a precursor, novel ordered mesoporous silica nanoparticles with a narrow pore size distribution and high crystallinity have been synthesized by various hydrothermal merging processes. Several architectures like chains, dumbbells, triangles, squares and flowers have been discovered. The linking mechanisms of these interacting silica spheres leading to the formation of ordered nano-structures are studied by HRTEM, HAADF-STEM and electron tomography and a plausible model is presented for several merging processes.