Thermal reduction by enhancing heat-generation phonon scattering can improve thermoelectric performance. In this paper, the phonon transport subjected to internal heat generation in two-dimensional nanoscale thermoelectric phononic crystals is investigated by a novel Monte Carlo method based on the universal effective medium theory, called the MCBU method. The present approach is validated. Compared with the universal effective medium theory method, the MCBU method is easier to implement. More importantly, the deviation of the computation time between the two methods can be ignored. With almost the same time cost, the present method can accurately calculate the effective thermal conductivity of complex geometric structures that cannot be calculated by the effective medium theory. The influences of porosity, temperature, pore shape and material parameters on thermal conductivity are discussed in detail. This study offers useful methods and suggestions for fabricating these materials with heat isolation and reduction.