A series of silica nanoparticles (SNP-1, SNP-2, SNP-3, SNP-4, SNP-5 and SNP-6) were synthesized in ethanol by the hydrolysis and polycondensation reaction of tetraethoxysilane with the aids of water initiator and ammonia catalyst and then investigated in a comprehensive manner in terms of morphological structure by using synchrotron transmission small-angle X-ray scattering and grazing incidence wide-angle X-ray scattering and combined together with dynamic light scattering, scanning electron microscopy, infrared spectroscopy and thermogravimetry. They were confirmed to be successfully synthesized as oblate amorphous ellipsoids (Re = 9.70~56.30 nm, equatorial radius; e = 0.78~0.80, ellipsoidicity) with sharp surfaces in single unimodal and narrow size distributions. The radial density profile details, including two-phases (i.e., less dense core and denser shell), were determined for the first time, in addition to a set of structural parameter details (radius of gyration, radius, core radius, shell thickness, and radius distribution). Larger particle was synthesized conveniently by higher loading of ammonia solution with respect to the silane monomer. The as-synthesized silica particles were found to undergo two-step mass loss behaviors in heat treatment up to 500 °C; the firststep loss took place below 120 °C due to removals of physically absorbed water molecules and possible solvent residues and the second-step loss above 180 °C occurred by removals of water and ethanol byproducts due to the post condensation reactions of hydroxy and ethoxy residues.