The invention relates to a control system of a super cleaning scrubbing machine for all-glass injectors. The control system comprises a processor, an outlet photoelectric sensor, an inlet photoelectric sensor, a pipe body photoelectric sensor used for identifying needle cores and needle sleeves and recording the total feeding number of the needle cores and the needle sleeves, a pipe head photoelectric sensor and a Hall sensor used for identifying the positions of U-shaped or C-shaped bayonets, corresponding to the needle cores or the needle sleeves, of a first washing divided wheel. The control system of the super cleaning scrubbing machine for the all-glass injectors is reasonable in structure, convenient to use, ingenious in design and advanced in technology.