The invention relates to a self-cleaning parallel filtration system, which includes a cleaning agent pot, a filter, a standby filter and a waste liquid receiving pot. Both sides of the filter and the standby filter are respectively provided with a material input pipe and a material output pipe, the filter and the standby filter are connected to one end of the material input pipe, the material input pipe is also in connection with a material input main pipe, the material input main pipe is equipped with a second valve, a cleaning agent circulation pipe and a first standby pipe, the filter and the standby filter are connected to one end of the material output pipe, the material output pipe is also connected to a material output main pipe, the material output main pipe is equipped with a sixth valve, a waste liquid circulation pipe and a second standby pipe, and the material input main pipe and the material output main pipe are both in connection with a pressure measurement pipe. The system provided by the invention realizes switching to the standby filter when the filter is in a saturated blocking condition to perform ceaseless filtration, also ensures integration of the filtration and self-cleaning process, has no leakage pollution, improves safety, and saves energy and cost.