This study investigated the performance and optimal operating conditions of a pilot-scale centrifugal separator for low-grade diatomite purification using response surface methodology (RSM). The individual and interactive effects of the feeding concentration (mass concentration of solids in the feeding slurry), centrifugal speed, feeding rate, and feeding time on the mass concentrations of centrifugal overflow and the SiO2 contents of centrifugal concentrate was investigated by RSM. Two second-order polynomial equations between the response and independent variables were proposed to describe the influence of different variables on the mass concentrations of the centrifugal overflow and SiO2 contents of centrifugal concentrate. It is indicated that the feeding concentration has the greatest influence on the tailing concentration. The operating conditions of the centrifugal separator were further optimized and the SiO2 content of purified diatomite was increased from 80.17% to 86.89% under the optimal conditions. Compared with raw minerals, the purity and porosity of diatomite were significantly improved after purification from chemical, x-ray diffraction (XRD), and scanning electron microscopy (SEM) analyses. It is concluded that this type of pilot-scale centrifugal separator is a potentially reliable instrument for low-grade diatomite purification at low cost in the industry.