The existing traditional drinking water disinfection technology relies mainly on chlorine disinfection alone, which has high disinfection efficiency and can effectively inactivate most of the microorganisms in the water. However, it produces a series of harmful disinfection by-products (DBPs). Therefore, it is very necessary to study an efficient and environmentally friendly disinfection technology for drinking water. For this purpose, a novel continuous-flow ultrasound (US)/chlorination water treatment system was designed and developed. Escherichia coli (E. coli), Bacillus subtilis (B. subtilis), and Staphylococcus aureus (S. aureus) were selected as indicators of water treatment effects to (1) investigate the disinfection effects of different bacteria by US treatment alone at different single or dual frequencies; (2) explore the disinfection effects of US pretreatment with 8 mg/L NaClO on different bacteria to assess the promoting effects of US pretreatment; and (3) identify the optimum system process to satisfy the national standard for drinking water quality. Results showed that the dual-frequency US had better inactivation effects compared with single-frequency US, although it could not achieve an ideal disinfection level (complete disinfection). Further, 17 + 33 kHz dual-frequency US pretreatment had obvious enhancement of the disinfection efficiency, where 3.85 (E. coli), 3.65 (S. aureus), and 3.52 (B. subtilis) log reduction were achieved when 8 mg/L NaClO disinfection lasted 10 min, and finally all three bacteria achieved 4 log reduction after 30 min. Moreover, the treated water satisfied the Chinese national standard for drinking water quality, in which the residual chlorine concentration was below 4 mg/L. The utilization efficiency of disinfectant was improved approximately 40% by 17 + 33 kHz US pretreatment.