In this work, we simulate a fiber mode-division multiplexing (MDM) transmission system with mode-dependent loss (MDL), and simultaneously explore the impact of MDL and burst perturbation on system performance. The impact of MDL on a 4×4 MDM transmission system is analyzed with fast perturbation of different intensities applied. Adaptive algorithms containing least mean square (LMS) and recursive least square (RLS) routines are used for fast channel compensation. The performance of these channel-compensation algorithms is calculated using mean square error (MSE). Simulation results show that MDL degrades system performance. Both LMS and RLS algorithms can compensate for the effects of dynamic perturbation on the system; however, MDL causes system performance to change greatly after compensation, i.e., the variance of MSE varies greatly.