Ultraviolet (UV) disinfection is an early discovered technology that is currently and widely used for water treatment and food hygiene treatment. A newly emerging technology of UV disinfection, that is, UV light-emitting diodes (UV-LEDs), has aroused considerable research attention. UV-LEDs feature numerous advantages compared with traditional UV mercury vapor lamps and are expected to replace traditional UV lamps. Researchers currently perform studies to obtain data and develop methods for UV-LED water treatment systems. This article analyzes the latest research status and discusses the types of inactivation factors, such as the wavelength selectivity of UV light source, control of UV dose, effect of inactivation rate constant (K) (cm ² /mJ), working mode of water sample, external auxiliary system, and UV sensitivity of pathogenic bacteria in water. The wavelengths of approximately 260 and 280 nm normally feature strong inactivation characteristics. When compared with the approximately 260 nm wavelength chip, the around 280 nm wavelength chip proves to be a better choice as its higher wavelength light power can result in faster disinfection capacity of bacteria. UV dose can also be used as the reference value for disinfection of drinking water, whereas the inactivation rate constant (K) (cm ² /mJ) varies with different microorganism internal structures. Changing the working mode or adding an auxiliary system can also enhance the inactivation effect in water treatment system settings. In addition, we can compare the inactivation capacities of several pathogens as follows: ΦX174 > Escherichia coli > T type bacteriophage > Bacillus subtilis > MS2 or Qβ > human adenovirus. The in-depth investigation and discussion of inactivation factors and the mechanism of action in UV-LEDs water treatment systems will establish a more efficient UV-LED disinfection method in the future, provide a guiding direction, and promote the standardization and normalization of pathogen inactivation mechanism in UV-LED water treatment systems.