The present invention provides a particle detection system and a detection method of a particle which can cope with a change in the measurement environment. The particle detection system of the present invention includes a flow path (2) for flowing a sample liquid containing particles, an inspection device (100) including a light source, a light detection unit, and a denoising filter, the light source examining the sample liquid and a light detector that detects a reaction light generated by particles irradiated with inspection light and emits a measurement signal that removes noise from the measurement signal, a flow meter (200) that measures a sample liquid An input device (402) that receives a measured flow rate; an input device (402) that receives a frequency of a noise to be removed by the noise canceling filter; and a control unit (301) that controls the frequency of the noise (402) to control the frequency of noise to be removed by the denoising filter.