The mechanism of a new optical function device——photonic crystal (PC) filter is discussed. Subsequently, the basic theory for encoder/decoder in optical code division multiple access (OCDMA) system based on multiple channel PC filter consisting of band-pass filter and band-stop filter is proposed. Light signals are divided into several chips by the defect resonate cavity to encode/decode the user signals in frequency domain, according to the coupled-mode theory. Thus, the decoder in 2D-OCDMA can be performed. A waveguide decoder/encoder in OCDMA system consisting of three-channel photonic crystal filter, whose wavelength centered at 1527.70, 1551.10, 1570.00 nm is designed. To elevate the transmission efficiency, an extra defect is attached in at the sideway of the bus waveguide. As a results, the efficiency of the second chip is up to 95%. In emulation, the full width at half maximum is 0.3 nm, so there won′t be interference between signals in each channel. Also, energy loss in the process of decoding/encoding by PC waveguide encoder/decoder is small, which plays an important part in remote communication.