Mini-magnetorheological damper is modeled using dissipative particle dynamics method, as a molecular modeling technique by applying various arrangement patterns of rough sections on the surface area of piston as four proposed scenarios of A, B, C, and D to obtain optimal damper performance. Modeling is developed to achieve 10-N damping force utilized in micro-machines and compared to experimental results that show good conformity. Weierstrass–Mandelbrot function is used to apply rough surface profile on the piston, and bounce back boundary condition is utilized as no-slip boundary condition. Results of modeling show that 140-CG magnetorheological fluid is suitable as the agent fluid. Also, it is observed that by increasing fractal dimension of roughness profile, damping force has an initial enhancement and then trends to a constant value. Results shown by utilizing Bouc–Wen model and genetic algorithm method and fractal dimension of roughness profile of 1.5 using at the beginning and the end of the piston as presented in scenario B; by applying 20% magnetic field strength, considered damping force of 10 N is achieved within 2 s, while under conventional conditions, using the smooth surface area of piston, more damping time is needed and more electrical energy is used than the developed model.