Thermal reduction by enhancing heat-carrying phonon scattering can improve thermoelectric performance. In this paper, the phonon transport in two-dimensional nanoscale thermoelectric phononic crystals is investigated by frequency-dependent Monte Carlo simulations. The dispersion curves of thermal wave propagating in phononic crystals are calculated based on a nonlinear regression model. And the influence of geometric parameters on dispersion curves and phonon transport is discussed in detail. The results indicate that the pore configuration and porosity have remarkable influence on the phonon transport. In addition, the dispersion curves are primarily controlled by the pore placement and temperature. This study offers useful suggestions for fabricating these materials with heat isolation and reduction.