Partial root-zone drying during irrigation (PRD) has been shown effective in enhancing plant water use efficiency (WUE), however, the roles of chemical signals from root and shoot that are involved and the possible interactions affected by nitrogen nutrition are not clear. Pot-grown cotton ( spp.) seedlings were treated with three levels of N fertilization and PRD. The concentrations of nitrate (NO), abscisic acid (ABA) and the pH value of leaf and root xylem saps, biomass and WUE were measured. Results showed that PRD plants produced larger biomass and higher WUE than non-PRD plants, with significant changes in leaf xylem ABA, leaf and root xylem NO concentrations and pH values, under heterogeneous soil moisture conditions. Simultaneously, high-N treated plants displayed larger changes in leaf xylem ABA and higher root xylem NO concentrations, than in the medium- or low-N treated plants. However, the WUE of plants in the low-N treatment was higher than that of those in the high- and medium-N treatments. PRD and nitrogen levels respectively induced signaling responses of ABA/NO and pH in leaf or root xylem to affect WUE and biomass under different watering levels, although significant interactions of PRD and nitrogen levels were found when these signal molecules responded to soil drying. We conclude that these signaling chemicals are regulated by interaction of PRD and nitrogen status to regulate stomatal behavior, either directly or indirectly, and thus increase PRD plant WUE under less irrigation.