Size, morphology, and crystalline phase of nanoparticles determine the properties of nanostructured materials. Therefore, the mastery of controlling properties ultimately requires the control of size, morphology, and phase of nanoparticles. From various aerosol methods, highly pure nanoparticles can be produced; however, agglomeration has been considered as almost unavoidable when nanoparticles are generated at high concentrations that are necessary for a practical application. Efforts to control, agglomeration have had only limited success. Here we report that the enhancement of coalescence of nanoparticles using laser beam irradiation on aggregates formed in flames can be a solution for this problem and successfully controls the size, morphology, and crystalline phase of high concentration nanoparticles of silica and titania. We demonstrate this principle by not only synthesizing smaller and unagglomerated nanoparticles, but also generating them in high concentrations. In addition, we show that the present method is capable of even controlling the crystalline phase of titania nanoparticles. Surprisingly, stable rutile titania particles have been transformed into metastable anatase and the weight percent of each phase could be controlled.