Secondary electron yield (SEY) is a dominant factor in determining the multipactor threshold. In this study, we analyzed the secondary roughness effect of surface microstructures for plastic dielectric on SEY reduction and multipactor mitigation. A single ridge waveguide (SRW) operating in Ku-band, filled with PTFE or PI, was designed with a dielectric-metal multipactor gap. By employing a femtosecond laser, periodic microstructures were fabricated on PTFE and PI surfaces to suppress SEY. The SEY peak values of PTFE and PI decreased from 2.05 to 1.40 and 1.37 to 1.07 by the porous surface. The surface morphologies and cross-sectional images of the porous PTFE and PI demonstrated the existence of secondary roughness structures. Via simulation, we obtained multipactor thresholds of 8496 W, 12374 W, and 9397 W for the SRWs filled with untreated PTFE surface, ideal porous surface (without secondary roughness), and real porous surface (with secondary roughness). Similar works were implemented for the PI-filled SRWs, resulting in simulated multipactor thresholds of 7640 W, 11327 W, and 9433 W. The results indicate that the multipactor effect may not be effectively suppressed under the influence of secondary roughness structures such as plastic velvet and foam. Besides, simulation works indicated that the radio frequency electric field could extract secondary electrons from the microstructures, weakening the mitigation effect of microstructures on multipactor. The impact of surface charging on electron motion was also analyzed by considering energy distribution. It was suggested that the surface microstructures of plastic dielectrics lead to a decrease in the surface charge density and the electrostatic field strength, weakening the self-extinguishing effect and lowering the multipactor threshold. This study provides an in-depth analysis of the effect of secondary roughness on SEY and multipactor for organic dielectrics, which makes significant sense for the further investigation of dielectric multipactor.