In recent years, ultraviolet technology for drinking water disinfection has experienced rapid growth in North America and Europe, driven by the needs of disinfection by-product reduction and control of emerging pathogens such as Cryptosporidium which are resistant to chlorination. Tsinghua University has performed some work based on a pilot-scale UV system in Dongguan. The aim of this study was to evaluate the efficacy of UV systems for drinking water under pilot-scale conditions (continuous flow system) and to compare with the collimated-beam results in the laboratory for the same water quality. The experiment results showed that (1) UV was effective against E. coli and TBC. B. substilis and MS2 were more UV-resistant, especially when UVT was below 90%. (2) The inactivation of micro-organisms by UV could be described by first-order kinetics using fluence–inactivation data from laboratory studies in CB tests for a certain fluence range. No inactivation at low fluences (shoulder) and no further increase of inactivation at higher fluences (tailing) was observed for some challenge micro-organisms. (3) Water quality and UV sensitivity of the micro-organism influenced the inactivation rate. (4) For the daily monitor results of 13,000 h, UV could be a stable disinfection manner for total coliform and TBC. (5) The lamp intensity online monitor showed that the lamp efficiency decay was limited to within the first 12,000 h.