The optical properties and performance of the two-dimensional photonic crystal (2D PhC) filters at normal incidence were simulated, and the best geometric parameters were obtained with the help of a global optimization program. The honeycomb structure has better performance, including high in-band transmittance, high out-band reflectance, and low parasitic absorption. The power density performance and conversion efficiency can reach 80.6% and 62.5%. Furthermore, the deeper cavity structure and multi-layer structure were designed to improve the performance of the filter. The deeper one can reduce the influence of transmission diffraction, increases the power density performance and conversion efficiency. The multi-layer structure reduces the parasitic absorption significantly and increases the conversion efficiency to 65.5%. These filters have both high efficiency and high power density, avoid the challenge of high-temperature stability faced by emitters, also easier and cheaper to fabricate compared to the 2D PhC emitters. These results suggest that the 2D PhC filters can be used in thermophotovoltaic systems for long-duration missions to improve the conversion efficiency.