This study investigates the influence of roughness on the transient flow behavior in the chamber based on the performance requirements of the pump rotor–stator chamber, aiming to elucidate the mechanism of roughness in real operating conditions. Three-dimensional models under two types of flow (centrifugal and centripetal) are developed, and transient numerical analyses are performed through numerical simulation and experimental validation. The results show that roughness significantly accelerates turbulence development in centrifugal through-flow, particularly in the middle- and high-radius regions, increasing the turbulent kinetic energy by approximately 18% compared to smooth surfaces. Transient flow analyses indicate that roughness leads to an overall pressure drop of around 10% within the cavity while facilitating the formation of high-pressure zones near the rotor. In centrifugal flow, high-pressure regions develop rapidly in the high-radius area, resulting in a stepped pressure distribution with a peak pressure increase of 12% at the outermost radius. In centripetal flow, the pressure distribution remains more uniform, yet significant pressure rise trends emerge over time, with pressure increasing by 8% due to the presence of roughness. This study presents a systematic analysis of the effects of roughness on transient flow characteristics in rotor–stator cavities across two flow modes for the first time, providing valuable insights for optimizing pump design and performance under real-world conditions.