The primary objective of this study is to evaluate the representation of the energy budget for irrigated maize crops in soil–vegetation–atmosphere transfer (SVAT) models. To this end, a comparison between the original version of the interactions between the soil–biosphere–atmosphere (ISBA) model based on a single-surface energy balance and the new ISBA-multi-energy balance (ISBA-MEB) option was carried out. The second objective is to analyze the intra- and inter-seasonal variability of the crop water budget by implementing ISBA and ISBA-MEB over six irrigated maize seasons between 2008 and 2019 in Lamasquère, southwest France. Seasonal dynamics of the convective fluxes were properly reproduced by both models with R2 ranging between 0.66 and 0.80 (RMSE less than 59 W m−2) for the sensible heat flux and between 0.77 and 0.88 (RMSE less than 59 W m−2) for the latent heat flux. Statistical metrics also showed that over the six crop seasons, for the turbulent fluxes, ISBA-MEB was consistently in better agreement with the in situ measurements with RMSE 8–30% lower than ISBA, particularly when the canopy was heterogeneous. The ability of both models to partition the evapotranspiration (ET) term between soil evaporation and plant transpiration was also acceptable as transpiration predictions compared very well with the available sap flow measurements during the summer of 2015; (ISBA-MEB had slightly better statistics than ISBA with R2 of 0.91 and a RMSE value of 0.07 mm h−1). Finally, the results from the analysis of the inter-annual variability of the crop water budget can be summarized as follows: (1) The partitioning of the ET revealed a strong year-to-year variability with transpiration ranging between 40% and 67% of total ET, while soil evaporation was dominant in 2008 and 2010 due to the late and poor canopy development; (2) drainage losses are close to null because of an impervious layer at 60 cm depth; and (3) this very specific condition limited the inter-annual variability of irrigation scheduling as crops can always extract water that is stored in the root zone.