Green macroalgal blooms have occurred in the Yellow Sea for 13 consecutive years since 2007. However, effective control methods have not yet been successfully developed. Ulva prolifera attached on Pyropia aquaculture rafts was identified as the main source of the blooms, thus, eliminating the attached Ulva from the rafts should be the most efficient method to prevent and control these blooms. In this study, we designed a new molecular marker (rps2-trnL) to identify U. prolifera collected from the aquaculture site. Samples identified as U. prolifera were cultured, and different concentrations of sodium hypochlorite (NaClO) solution (0.2, 0.4, 0.6, 0.8, and 1.0%) were used to kill the alga. The measured chlorophyll content, light quantum yield, and photosynthetic oxygen release rate data from the laboratory experiment suggested that the appropriate concentration of NaClO solution should be 0.6–1.0%. To carry out a small-scale field trial, we developed a device that can spray NaClO on Ulva blades and recycle the residual liquid. Results showed that only the 1.0% NaClO solution could quickly kill the Ulva in outdoor experiments. During the treatment, very little NaClO dripped on the tidal flat, which indicated that the recycling device avoided a potential negative impact of residual solution on the marine ecosystem. By the beginning of November 2019, the Pyropia aquaculture area treated by NaClO was about 13,000 ha, covering about one-third of the total area at the coast of Jiangsu Province. Monitoring by an unmanned aerial vehicle showed that very little attached Ulva was present on the ropes after NaClO treatment, which indicated that it was an effective method to control the green tide. Also, the range of residual active chlorine within seawater during the treatment was only from 0.003 to 0.012 mg/L, which complied with Chinese national standards. However, further monitoring of the formation process of green tides should be conducted in future years to evaluate the effect of NaClO treatment.