Nanophononic metamaterials (NPM) have received surging research attention for thermal conductivity modification. The local resonance hybridization mechanism of NPM is of great significance to the performance optimization of heat flux regulation devices. In this Letter, using silicon nanofilm with a periodic array of nanopillars as example, we systemically studied the phonon localization effect and heat flux regulation. The results demonstrate that the phonon localization effect produced by the nanopillars is mainly concentrated in the region close to surface layer. Moreover, the effects of nanopillar height, spacing, and atomic mass of atoms in the nanopillars on the localization are also explored. Finally, the relationship between phonon localization and heat flux density is demonstrated through non-equilibrium molecular dynamics calculations. This study provides not only the better understanding of the phonon resonance hybridization mechanism in nanophononic metamaterials but also useful guidelines for the design of nanoscale heat flux regulation devices.