Deficit irrigation (DI) was acknowledged as an effective technique to improve water use efficiency (WUE) without significant yield reduction. In this study, a 3-year field experiment was conducted in Northeast China during 2017–2019 to investigate the combined effects of 3-week DI from 3-leaf stage and N fertilization on maize seedling growth and determine the resulting impacts on silking growth and yield formation, N use efficiency (NUE) and WUE. Results showed that seedling-stage DI decreased leaf area and photosynthesis, thus significantly limited shoot and root dry biomass for maize seedling, compared to well-watered (WW) plants. In 2017 and 2019, seedling-stage DI positively improved seedling growth with higher root: shoot ratio and enhanced drought tolerance, under higher initial soil water contents (SWC) with sufficient precipitation before DI. The DI-primed plants showed similar or better performances on reproductive growth, grain yield, WUE and NUE compared to WW plants, even experiencing heavy rainfall or drought stresses around the silking stage. However, the contrasting results were observed in 2018 with negative DI effects on seedling and silking growth and final yield, probably due to less rainfall and lower SWC before DI. In all 3 years, N fertilization had significant compensatory effects on limited seedling growth under DI, and its effect was much less in 2018 than other years due to adverse early climate. The principal component and correlation analysis revealed maize silking growth, grain yield, NUE and WUE were strongly related to the seedling growth as affected by water and N managements under various climatic conditions. In conclusion, a short-term and moderate DI regime—adopted at the seedling stage under higher initial SWC and coupled with an appropriate N fertilization—is beneficial to control redundant vegetative growth while optimizing root development, therefore effectively improving drought tolerance for maize plants and achieving higher grain yield, WUE and NUE.