An ultrasound/ultraviolet (US/UV) baffled reactor was developed to fill the gap in ultraviolet (UV) disinfection associated with disinfection efficiency. According to the previously selected operational condition, a continuous-flow US/UV baffled reactor was continuously operated in a wastewater treatment plant at a pilot scale for nearly three months, and the disinfection influent and effluent were analyzed, including fecal coliforms, Escherichia coli, and fecal streptococci. The US/UV baffled reactor could guarantee a high effluent disinfection performance in terms of fecal coliforms removal even with the fluctuation of the secondary effluent. All the disinfected effluents satisfied the requirement of the “Pollutants Discharge Standard of Municipal Wastewater Treatment Plant in China” (fecal coliforms below 1000CFU/L for class 1A), and 87% of the tested fecal coliforms concentration in the disinfected effluent was below 100CFU/L, nearly eliminating all fecal coliforms. Further analysis of the E. coli and fecal streptococci showed the broad disinfection ability and high disinfection efficiency of the US/UV baffled reactor. The flexibility of the specific energy consumption for the disinfection system depends on the water quality.