The cleaning unit is a key functional component of grain combine harvesters, yet its operating parameters are still predominantly adjusted according to operator experience, resulting in limited adaptability to fluctuating working conditions. To enhance the intelligence and stability of the cleaning process, this study develops a fuzzy control approach supported by data-driven performance modeling. Based on multi-condition bench experiments, feeding rate, fan speed, cleaning sieve vibration frequency, and sieve opening were selected as input variables. Gaussian Process Regression (GPR) models were established to describe the nonlinear relationships between operating parameters and cleaning loss rate and impurity rate, and impurity rate was inferred online to compensate for the absence of a reliable sensor. Taking feeding rate variation as the primary disturbance, a dual-input fuzzy control strategy was designed using loss rate monitoring and model-predicted impurity rate as feedback signals. Simulation and bench test results show that, under small and moderate load disturbances (±20% and ±35%), the proposed method reduces either impurity rate or cleaning loss rate through coordinated parameter adjustment. Under large disturbances (±50%), performance deterioration cannot be fully eliminated, but its extent is alleviated compared with open-loop conditions.