The invention discloses a system for automatically capturing and counting CD4+T lymphocytes based on magnetic beads. The system comprises a micro-fluidic chip and a matching drive unit. The micro-fluidic chip includes a layer of cover plate and a layer of structure plate, and mainly comprises functional modules of a reaction chamber, a waste liquid chamber, and a counting area. Through the reaction chamber, under the control of the matching drive unit, the magnetic beads can fast capture CD4+T lymphocytes in a detection sample, and subsequent fluorescence labeling and cleaning of the CD4+T lymphocytes can be carried out. The waste liquid produced in each step of a reaction flows in the waste liquid chamber for storage, so that the pollution from detection is avoided. Finally, under the control of the matching drive unit, the CD4+T lymphocytes provided with fluorescence labels are distributed in the counting area of the chip to form a single-layer distribution detection system. Through utilization of high-sensitivity fluorescence detection technology, the single-layer distribution detection system of CD4+T lymphocytes is subjected to fluorescence signal analysis, and the CD4+T lymphocytes are automatically counted.