Onion is sensitive to soil water stress and nitrogen limitations, causing a marked reduction in yield and bulb quality. A field trial was set in the winter seasons of 2016–17 and 2017–18 to evaluate the effects of three micro-sprinkler irrigation levels at 0.6, 0.9 and 1.2 ratios of crop evapotranspiration (ETc) and four nitrogen levels at 0, 75, 100 and 120% of the recommended nitrogen dose (RDN), including surface irrigation at 40 mm cumulative pan evaporation (CPE) with 100% RDN (SN) using an augmented strip plot design on water and N distribution in soil, their productivities, onion yield and economics. Results indicated that the root zone water content increased by 5.2% for 1.2 ETc, and 1.4% for 0.9 ETc over the cropping period, but declined by 1.5% for 0.6 ETc with micro-sprinkler irrigation compared to surface irrigation with nitrogen fertilization (SN). The largest total root zone water depletion was in 1.2 ETc (16.7%), followed by SN (15.3%) and 0.9 ETc (15.0%). The high irrigation regime produced the maximum yield and nitrogen productivity, whereas deficit irrigation displayed the greatest water productivity. However, the coupling of micro-sprinkler irrigation at 1.2 ETc and 120% RDN led to an increase of onion bulb yield (22.6%), water productivity (42.7%), plant N uptake (29.0%) and net income (30.6%) with maximum benefit-cost ratio (3.19) compared to SN. However, as this study was only based on two seasons, more field trials will be needed to confirm the optimum amount of water and nitrogen for winter onion.