An optical fiber secure communication apparatus and a data encryption method therefor are provided. The apparatus comprises a transmitter and a receiver being connected with each other via an optical fiber. The transmitter comprises a PPC processor unit, a field programmable gate array test board, a light-emitting module, an optical fiber coupler and a connection optical fiber. The receiver comprises a wavelength division multiplexer, a connection optical fiber, a photodetector, a field programmable gate array test board, a PPC processor unit and a signal output interface. At the transmitter end, two or more paths of input data are forwarded by the PPC, encrypted by the FPGA and then transmitted to the light-emitting module of two or more wavelengths for conversion from electrical signals into optical signals. At the receiver end, signals of two or more wavelengths enter the photodetector for conversion into electrical signals, which are decrypted by the FPGA and then forwarded by the PPC for output. With the present invention, the security of transmission data is improved and the difficulty in cracking data is increased.