The path toward realizing the potential of seasonal forecasting and its socioeconomic benefits depends heavily on improving general circulation model based dynamical forecasting systems. To improve dynamical seasonal forecast, it is crucial to set up forecast benchmarks, and clarify forecast limitations posed by model initialization errors, formulation deficiencies, and internal climate variability. With huge cost in generating large forecast ensembles, and limited observations for forecast verification, the seasonal forecast benchmarking and diagnosing task proves challenging. In this study, we develop a probabilistic deep neural network model, drawing on a wealth of existing climate simulations to enhance seasonal forecast capability and forecast diagnosis. By leveraging complex physical relationships encoded in climate simulations, our probabilistic forecast model demonstrates favorable deterministic and probabilistic skill compared to state-of-the-art dynamical forecast systems in quasi-global seasonal forecast of precipitation and near-surface temperature. We apply this probabilistic forecast methodology to quantify the impacts of initialization errors and model formulation deficiencies in a dynamical seasonal forecasting system. We introduce the saliency analysis approach to efficiently identify the key predictors that influence seasonal variability. Furthermore, by explicitly modeling uncertainty using variational Bayes, we give a more definitive answer to how the El Nino/Southern Oscillation, the dominant mode of seasonal variability, modulates global seasonal predictability.