To further increase energy conversion efficiency of micro thermophotovoltaic system, a 1-D Si/SiO2 photonic crystal filter was set in the system to ensure recycle of long wavelength radiation energy. The basic structure design and corresponding optical characteristics were obtained through optical thin film theory and transmission matrix method, and an improved design [1.10(L/2HL/2)](L/2HL/2) 3 [1.10(L/2HL/2)] [0.95(L/2HL/2)](L/2HL/2) 3 [0.95(L/2HL/2)] was developed according to the narrower first reflection band of basic structure by method of multilayered film superposition, which could extend the first reflection band to 2~4μm and also had a transmission of 0.95 in the pass band. By perfecting the energy transition computational model, calculation results showed that the using of filter could effectively lower the burden of cell cooling, while at the same time boosted the temperature of radiation wall so as to raise system output performance. System output power density and total efficiency reached to 5.46W and 2.6% when using the improved structure filter at mixture flux of 1500mL/min, which was 5.7% higher than the result of using basic structure filter.