The invention discloses a flow cytometer full-automatic cleaning system, and belongs to the technical field of multifunctional rapid detection devices special for clinical medical physiology, biochemistry, pathological examination. The system comprises a flushing liquid tank, a first cleaning pipeline, a first electromagnetic valve, a first cleaning branch pipe, a second electromagnetic valve, a front pool, a rear pool, gem holes, a first liquid inlet pipe, a second liquid inlet pipe, a third electromagnetic valve, a sampling needle, a swab, a fourth electromagnetic valve, a second cleaning branch pipe, a third cleaning branch pipe, a set of reaction cup cleaning needles, a set of liquid absorption needles, a second liquid drainage pipe and a waste liquid drainage outlet. According to theflow cytometer full-automatic cleaning system, by arranging a reasonable cleaning agent circulation pipeline, all units of a flow cytometer can be cleaned, cleaning efficiency is improved, cleaning agent using efficiency is improved, the cleaning effect of the flow cytometer can be ensured, and use is safe and reliable.