Fertilizers injected into the drip irrigation system may contribute to serious clogging, which occurs due to multiple factors, including water quality, water condition, hydraulic parameters and system design. To better understand the causes and process of emitter clogging of fertigation at different irrigation water temperature levels, laboratory experiments were conducted to investigate the effects of irrigation water temperature on the sensitivity of emitter clogging. Three different particle gradations and three different fertilizer concentrations were investigated through the intermittent drip irrigation method in summer and winter, respectively. Experiment results showed that the temperature of irrigation water was an important factor causing clogging with remarkable coupling effect with water quality. The anti-clogging performance of emitter in summer was always better than that in winter for both scenarios of fertilization and no fertilization. The acceleration of drip clogging with fertilization was affected by the sediment gradation and the season. When the content of sediment particles (with diameter of 0.034~0.1 mm) became high, the fertilizer concentration could be more sensitive to clogging in winter than that in summer. The fertilizer concentration became more sensitive to clogging when the content of sediment particles (with diameter of 0~0.034 mm) were high in summer than that in winter. The number of effective irrigation frequency in summer was 1.26~1.43 times as much as it was in winter. However, the irrigation water temperature could not change its effect on clogging caused by sediment gradation and fertilization concentration. Therefore, it is recommended that the irrigation frequency can be reduced when the temperature stays low, and the fertilizer concentration can be controlled at a low level when irrigation is applied with fertilizer.