Dispersing nanomaterials can effectively improve the thermal energy storage performance of molten salts. However, research on such improvement mechanism is still immature, as the understanding of the performance improvement levels induced by different nanoparticles has not been consistent. Using silica nanoparticles as additives, this work prepares nine molten salt nanofluids by aqueous solution method with the use of potassium nitrate, sodium nitrate, and their binary mixture as base salts. The key thermal performance of these nanofluids are evaluated through different characterization approaches, such as differential scanning calorimetry, thermal gravimetric analysis, laser flash analysis, and scanning electron microscopy for microstructural characteristics. The possible performance enhancement mechanism caused by silica nanoparticle is also explored. Results show that, for these nine molten salt nanofluids containing silica nanoparticles, the change in the melting point is negligible. The potassium nitrate salt dispersed with 20-nm silica nanoparticles achieve the highest performance improvement not only in latent heat but in specific heat and thermal conductivity, while sodium nitrate salt nanofluids reach maximum improvement at their decomposing temperature. The improvement level can be associated with the electronegativity of alkali ions. Cloud nuclei cause microstructure differences among molten salt nanofluids and may be the main reason for the thermal performance enhancement of the molten salt nanofluids.