The invention belongs to the technical field of agricultural engineering, and relates to an anti-clogging technology for an inserted irrigation emitter, in particular to a separation-treatment-based chemical anti-clogging method for an inserted irrigation emitter. The method comprises conventional physical flushing and scrubbing methods and a chemical chloride or acid addition method, wherein chloride addition treatment is as follows: for clogging caused by fungus and alga precipitates, liquid sodium hypochlorite NaC10 and solid powdery calcium hypochlorite Ca(C10)2 are adopted, the chloride addition concentration is 500mg/L or 600mg/L, the inserted irrigation emitter is impregnated for 15 or 30 minute, and then a physical method is adopted for treatment; add addition treatment is as follows: for clogging caused by carbonate precipitates, CaCO3 and MgCO3 are adopted, the acid addition concentration is 0.3mg/L or 0.4mg/L, the inserted irrigation emitter is impregnated for 15 or 30 minutes, and then a physical method is adopted for treatment. The method has the advantages that the method is convenient to implement, and can be popularized and used in a large area; chemicals are not required to be dissolved in an irrigation water source, so that soil pollution is avoided; the treated irrigation emitter can be recycled, so that the running cost of equipment is lowered.