The objective of this study was to investigate the comparative effects of alternative partial root-zone irrigation (PRI) and deficit irrigation (DI) on fertilizer-N use efficiency in tomato plants under mineral N and organic N fertilizations. The plants were grown in split-root pots in a climate-controlled glasshouse and were subjected to PRI and DI treatments during early fruiting stage. When analyzed across the N fertilizer treatments, PRI treatment led to significantly higher N yield, agronomic N use efficiency (ANUE), and apparent N recovery efficiency (ANRE) as compared with the DI treatment, indicating significantly higher fertilizer-N use efficiency and soil N availability as well as enhanced plant’s N acquisition ability in the PRI treatment. Analysis across the irrigation treatments showed that the mineral N fertilizer treatment (MinN) significantly increased N yield, ANUE and ANRE relative to the organic N fertilizer treatment (OrgN). Compared with DI, the rhizosphere and bulk soil mineral N content in the soil were significantly lowered in the PRI treatment, indicating the enhanced root N uptake efficiency. It is suggested that PRI-enhanced soil water dynamics may have increased soil nitrate mass/diffusive flow to the root surfaces and root N uptake efficiency in the wetting soil and stimulated soil N mineralization and plant N demand, contributing to the improved fertilizer-N use efficiency in the PRI relative to the DI treatment.