Globally, water-saving irrigation plays a vital role in agricultural ecosystems to achieve sustainable food production under climate change. Irrigation under mulch (IUM) system has been widely used in modern agricultural ecosystems due to its high water use efficiency, but it remains unclear how each component of the water and energy processes responds to this agricultural management practice. Current modeling approaches are inadequate in investigating the impacts of IUM management on water-energy balance, which have shown more complicated than non-mulched management. Therefore, this study provided an explicit simulation of water and energy fluxes in IUM system using a process-oriented ecosystem model—CoupModel and the three years of the eddy covariance (EC) measurements. Based on Monte Carlo and the multiple model performance evaluation criteria, most of the model sensitive parameters were well constrained and 32 potentially important parameters, e.g., i_scovevap, the fraction of mulch coverage, were identified to characterize the impacts of plastic mulching on energy balance and water transport. After proper calibration, the coefficient of determination (R²) for measured and simulated soil temperature (T) and soil water content (SWC) was 0.79 and 0.60, respectively, and the R² for T and SWC during the validation period were 0.91 and 0.71, respectively. Furthermore, we found that there was a strong coupling between the parameters of the water and energy processes, which would restrict the simulation results due to the correlation between the parameters and the evaluation indices. This study presented a systematic model parameters calibration in the agricultural ecosystem implemented with IUM and provided with a more comprehensive understanding of the water and energy balance in cropland. These results would help agricultural model development with more detailed considerations of the water-saving management.