A new method was proposed to control Harmful Algal Blooms (HABs) by a biosurfactant sophorolipid. The effect of sophorolipid on the growth, motility, precipitation, and recovery of algal cells was investigated for four common HAB species, Scripsiella trochoidea, Prorocentrum minimum, Cochlodinium polykrikoides, and Heterosigma akashiwo. The motility and growth of algal cells were inhibited significantly at the concentration of 20 and 5 mg/l sophorolipid, respectively, and no recovery was observed under the above concentrations. The concentration of 20 mg/l sophorolipid was considered to be an effective concentration for the mitigation of HABs. A sedimentation test suggested that the maximum precipitation occurred at the end of 1 h, and the algicidal effect of sophorolipid was observed by a microscope. Comparative study showed that sophorolipid had marked algicidal capability. Analysis on biodegradability, toxicity, and cost effectiveness further demonstrated the potential of sophorolipid in future HABs mitigation.