Crop growth models are multi-outputs and can be valuable tools for the quanti cation of crop growth and production. However, these models usually require several input data, which are costly, time-consuming, and sometimes impossible to measure. These input parameters are mostly estimated by calibration and inverse solving. In this study, ve output variables of the AquaCrop model, including soil evaporation, crop transpiration, evapotranspiration, crop biomass at maturity, and grain yield, were investigated to study 47 genotypic input parameters on the output time series of the model for wheat in the Qazvin Synoptic Station. The SAFE toolbox in the Matlab environment was used to study the GSA and uncertainty of inputs and their impact on outputs. Applying the Monte-Carlo-based methods on closed-source models is not as easy as open-source models. The uncertainty in the outputs of the validated AquaCrop model in simulating wheat yield in the Qazvin Synoptic Station over 36 years was analyzed using the Generalized Likelihood Uncertainty Estimation (GLUE) method.The uncertainty in the outputs of the validated AquaCrop model in simulating wheat yield in the Qazvin station over 36 years was analyzed using the GLUE method. Using RMSE<0.9 as the threshold in a 95% con dence level, the best parameter sets included all the observations. Results showed that evaporation and yield are the least reliable outputs of the AquaCrop model that have not been calibrated, while others consider them reliable. After that, the new domain of each output was determined based on the two indexes. Then we modi ed the domain to reduce its size. Finally, the probabilistic behavior of each input on outputs were introduced by the Easy Fit software. The signi cant result of this study is that the probabilistic nature of the input parameter that is calibrated for a particular output variable can differ from other output variables. Also, when we trust a speci c run of the model (calibrated run) as observed data, the uncertainty bounds covering are very high. Finally, we utilized the GLUE to optimize multi-output models by introducing one unique, optimized PDF for each input parameter for all outputs estimated by collecting all accepted output series of all target outputs.