Programmable imager spectrometer can provide flexible data by changing the spectrum section number, central wavelength, spectral width and spatial resolution in orbit. Spectral calibration of imaging spectrometer plays an important role for acquiring accurate spectrum, two spectral calibration types are in essence: wavelength calibration and Full-width-half-maximum (FWHM). Base on the character of programmable imager spectrometer, designed a set of spectral calibration system. Wavelength calibration realized by utilizing the Monochromatic light of high precision monochromator, during the test, changed output parameters of monochromator according to the spectral bandwidth of imager spectrometer. The FWHM is constructed by a set of variable narrow spectrum lines that is output by tunable laser. Gaussian fitting algorithm is used to determine center wavelength and the FWHM of the characteristic spectrum line, Spectral pixels are calibrated by quadratic polynomial, standard spectroscopic lamp is used to verify wavelength calibration result accuracy. The calibration result indicates that FWHM is better than 2nm, the wavelength uncertainty is less than 0.6nm, meet the calibration requirements of programmable imaging spectrometer.