In order to design high stop-band loss photonic crystal stop-band filter (PCSBF) structure, performances of the structure are optimized by adjusting coupling length between the waveguide and rectangular resonator, the size of the rectangular cavity and inner m×n rods radii etc. Operational features of the PCSBF based on m×n rectangular resonator are qualitatively analyzed by using time domain CMT (Coupled-mode theory), and strong coupling stop-band loss transmission conditions of the PCSBF are obtained. Output performances of the PCSBF are studied by using FDTD method between 1440nm wavelength and 1625nm wavelength. Normalized stop-band spectra curves show that this kind of micro PCSBF possesses characteristics of high normalized stop-band loss, tunable stop-bands, flat top stop-bands and so on. It possesses potential application value in the removal of unneeded wavelengths in the fields of optical fiber communications and integration of optical paths.