The inducing mechanism of emitters clogging with fertigation was explored. A laboratory experiment was conducted to investigate the influence of three factors (fertilizer types, fertilizer concentration and flow path structure) on anti-clogging performance of drip emitters. The intermittent drip irrigation experiment was studied by using two flow path types of non-pressure compensating emitters (arc-shaped saw-tooth and cup-shaped saw-tooth), four levels of fertilization concentration (0.5%, 1.0%, 2.0% and 3.0%) and four types of fertilizer (urea, calcium superphosphate, potassium sulfate and water soluble compound fertilizer) and the system was allowed to run for 20 h. The mathematical analysis methods in combination with field scanning electron microscope (FESM), energy dispersive spectrometer (EDS) and X-ray diffraction (XRD) technology were then used to quantitatively and qualitatively analyze the variations of the emitter’s average relative flow rate, surface topographical characteristics and components of the clogging materials internal emitters. Results showed that fertilizer characteristic was an important factor in deciding the emitter clogging type and degree (P<0.01), and the influence of the two flow path structures on the accelerating effect of emitter clogging performance needed to consider the path structural size and style. The accelerating effect of fertilizer application on emitter was not obvious when the concentration of fertilizer solution was less than 0.5%. When the concentration was increased to 0.5%～2.0%, there were obvious changes in the quantities of outflow discharge occurred in phosphate-fertigation, which made it clog easily, followed with urea-fertigation, the applicability of potassium-fertigation and compoundfertigation was better than that of the former. When the concentration was risen to 2.0%～3.0% or higher, the clogging degree was so serious with ureafertigation, the flow rate was decreased by 1026%, which was significantly higher than those of phosphate-fertigation (7.85%), potassium-fertigation (4.07%) and compound-fertigation (2.74%). Fertilization can promote the clogging of the emitters. These fertilizer types had different water quality, hence resulting into different emitter clogging risk and inducing mechanism. Emitters clogging with urea fertigation were caused by the role of aggregation and adhesion with both crystallization of the molecular urea state and suspended particles in the water. The adsorption function that particulate impurities to phosphorus promoted flocculation while precipitation among solid particles was as a result of inducing mechanism of emitter clogging with phosphate fertigation. The main inducing mechanism for emitter clogging with potassium-fertigation was chemical precipitation because of the ion-exchange action, while emitter clogging with compound-fertigation had the lowest risk. Therefore, fertigation with different fertilizer types should adopt different emitter clogging controlling management strategy.