The invention provides a filter type two-waveband small ultraviolet omnidirectional imager system, relating to the field of an optical machine. The system comprises two ultraviolet wide waveband imagers, a narrow band filter, a filter wheel and a stepping machine, wherein each ultraviolet wide waveband imager comprises an N pyramid reflector, a wide waveband ultraviolet lens group, a CCD (charge coupled device) detector and an electronics system, wherein the wide waveband ultraviolet lens group, the CCD detector and the electronics system are arranged in front of the N pyramid reflector in sequence; the CCD detector is connected with the electronics system; a narrow band filter is arranged between the wide waveband ultraviolet lens group and the N pyramid reflector; the stepping motor is arranged between the two ultraviolet wide waveband imagers; the filter wheel is arranged on the stepping motor; and the narrow band filter is arranged on the filter wheel. The system uses the high-performance narrow band filter and the ultraviolet wide waveband imagers to perform large-range high-resolution detection on the atmosphere in the ultraviolet band under the star and in limb direction. The system is suitable for detecting the high space-time coverage of the middle atmosphere and near space.