According to the principles of Hadamard transform spectrometer and the slit diffraction characteristics, the influence of spectrometer entrance slit diffraction of Hadamard transform spectrometer on the measurement result was analyzed, for the diffraction case, the Hadamard transform spectrometer instrument structure matrix was studied, and the Hadamard transform spectrometer encoding/decoding method was established. The analysis of incident spectral verified the correctness of the coding/decoding. This method is very important for the high precision measurement of Hadamard transform spectrometer.