Drip irrigation is an important way to alleviate the global water shortage. However, the emitter-clogging issue of drip irrigation directly affects irrigation uniformity and operation efficiency, even disabling the whole system and reducing crop production. Currently, with the widespread use of saline water and large-scale utilization of fertigation, the issue with the chemical clogging of emitters has become more prominent. The poor uniformity of irrigation and fertilization distribution caused by emitter clogging results in salt damage and fertilizer loss due to the complex clogging mechanism. However, no extensive information on chemical clogging is available. Herein, we surveyed the latest research on chemical clogging caused by saline water irrigation and fertigation in drip irrigation systems and described the clogging mechanisms of the emitter by analyzing the key factors, clogging rules, and substances. We also present a framework of the control technologies for clogging based on physical, chemical, and biological methods. Finally, we present the current challenges of fertigation with saline water and technical trends of emitter clogging in the drip irrigation system. To conclude, the efficient integration of these three methods is critical to prevent and eliminate chemical clogging.