Improving the utilization efficiency of agricultural water resources serves as a fundamental strategy for alleviating agricultural drought and water scarcity and ensuring food security. Micro-ridge-furrow rain harvesting cultivation (MRF) boosts crop yields by increasing soil water storage, but its effect on winter rapeseed production remains unclear in seasonal arid regions. A field experiment was conducted to investigate the effect of MRF height (10 and 20 cm, denoted as H10 and H20, respectively) on the yield and water productivity (WPc) of winter rapeseed in seasonal arid regions of Southwest China, using conventional flat planting (CK) as the control. MRF had a greater soil water content (SWC) in the ridge furrow and better root and shoot growth than CK, increasing rapeseed yield by 15.09 % and WPc by 15.96 % (P < 0.05). MRF slightly improved the seed quality compared with CK by increasing the oil, protein, and glucosinolate contents by 3.59 %, 3.28 %, and 1.83 %, respectively. SWC in the ridge furrow was slightly 3.30 % greater under H20 than under H10. The root dry weight density, root length density, root surface area density, and root volume density under H20 increased by 13.10 %, 16.57 %, 15.91 %, and 11.84 %, respectively, compared with H10. The plant height (3.77 %), SPAD (1.40 %), stem diameter (8.69 %), aboveground dry matter (16.68 %), and yield components were higher under H20 than under H10. The seed yield, WPc, and economic benefits insignificantly increased by 6.78 %, 7.11 %, and 4.35 %, respectively, under H20 compared with H10. H20 partly improved the seed quality compared with H10, with the oil, protein, and glucosinolate contents increasing by 1.57 %, 1.91 %, and 0.85 %, respectively. Overall, a 20 cm MRF height is recommended for crop production to improve SWC, crop growth, seed yield, WPc, and economic benefits of winter rapeseed. The results provide a theoretical basis and technical support for the improvement of water conservation and efficiency in winter rapeseed production in seasonal arid regions.