The utility model relates to a counting system of a particle counter. The counting system comprises a comparer circuit and a counting circuit, wherein one input end of the comparer circuit is connected with the output end of a signal processing circuit, and the other input end of the comparer circuit is connected with a reference voltage; the comparer circuit is used for comparing a signal processed by the signal processing circuit with the reference voltage, and outputting a pulse signal with pulse width corresponding to the size of particles; the counting circuit comprises a pulse shaping unit for shaping the pulse signal and a programmable logic control unit; the input end of the pulse shaping unit is connected with the output end of the comparer circuit; and the input end of the programmable logic control unit is connected with the output end of the pulse shaping unit, and the programmable logic control unit is used for determining the size of particles and counting particles according to the pulse signal shaped by the pulse shaping unit. According to the counting system provided by the utility model, a system structure is optimized, the resolution, reliability, stability and anti-interference performance of the counting system are improved, and the cost and power consumption of the system are reduced.