Centrifugal cleaners are commonly used in the pulp and paper industry to separate contaminates from pulp fibers. To reveal the separation mechanism of cellulose fibers and impurities in a centrifugal cleaner, three-dimensional computational fluid dynamics (CFD) models were established based on experimental analyses with the inlet flow rate and outlet diameter as the variables. The incompressible three-dimensional Navier-Stokes equations were applied to describe the fluid motion. Numerical simulation results showed that an increased inlet flow rate could improve the efficiency by enhance of the centrifugal force on particles. Secondary swirling patterns were predominant for centrifugal cleaners with smaller lower outlets. The crowding effect played an important role in the separation of heavy contaminants, and the separating efficiency was proportional to the inlet flow rate and inverse proportional to the lower outlet diameter.