In consideration of the phase difference between the reflected electromagnetic wave and incident electromagnetic wave in the input waveguide of the filter, operational performances for different design conditions are analyzed by the coupled mode theory (CMT), then the filter structure based on photonic crystal 1×3 cavity is optimized. The characteristics of the filter are studied by using the FDTD method. Average peak wavelength normalized transmission of the 96 pass-bands obtained by adjusting locations of the tuning rods below 1×3 cavity is up to 89.6%. Average spacing between adjacent peak wavelengths is 1.25nm. Average band width of the filter and average quality factor of the cavity are 1.19 nm and 1 350.2, repectively. Tunable ranges of the dropping peak wavelengthes are between 1 534.04 nm and 1 653.16 nm. The results show that the filer has the characteristics of high normalized transmission, narrow band width, and stable wavelength signal dropping intensity etc. This structure has potential value in the designs of dense wavelength division demultiplexing (DWDDM) system, optical sensing device, and dense optical path integration etc.